Is the story true?

[David Lockmiller]

A few days before the President's death, Secretary Stanton tendered his resignation of the War Department. He accompanied the act with a heartfelt tribute to Mr. Lincoln's constant friendship and faithful devotion to the country; saying, also, that he as Secretary had accepted the position to hold it only until the war should end, and that now he felt his work was done, and his duty was to resign.

Mr. Lincoln was greatly moved by the Secretary's words, and tearing in pieces the paper containing the resignation, and throwing his arms about the Secretary, he said: "Stanton, you have been a good friend and a faithful public servant, and it is not for you to say when you will no longer be needed here." Several friends of both parties were present on the occasion, and there was not a dry eye that witnessed the scene.

"On the night of the 3rd of March, the Secretary of War, with others of the Cabinet, were in the company of the President, at the Capitol, awaiting the passage of the final bills of Congress. In the intervals of reading and signing these documents, the military situation was considered,—the lively conversation tinged by the confident and glowing account of General Grant, of his mastery of the position, and of his belief that a few days more would see Richmond in our possession, and the army of Lee either dispersed utterly or captured bodily,—when the telegram from Grant was received, saying that Lee had asked an interview with reference to peace. 

Mr. Lincoln was elated, and the kindness of his heart was manifest in intimations of favorable terms to be granted to the conquered Rebels.

"Stanton listened in silence, restraining his emotion, but at length the tide burst forth. 'Mr. President,' said he, 'to-morrow is inauguration day. If you are not to be the President of an obedient and united people, you had better not be inaugurated. Your work is already done, if any other authority than yours is for one moment to be recognized, or any terms made that do not signify you are the supreme head of the nation. If generals in the field are to negotiate peace, or any other chief magistrate is to be acknowledged on this continent, then you are not needed, and you had better not take the oath of office.'

"'Stanton, you are right!' said the President, his whole tone changing. 'Let me have a pen.'

"Mr. Lincoln sat down at the table, and wrote as follows:—

"'The President directs me to say to you that he wishes you to have no conference with General Lee, unless it be for the capitulation of Lee's army, or on some minor or purely military matter. He instructs me to say that you are not to decide, discuss, or confer upon any political question. Such questions the President holds in his own hands, and will submit them to no military conferences or conventions. In the mean time you are to press to the utmost your military advantages.'

"The President read over what he had written, and then said:—

"'Now Stanton, date and sign this paper, and send it to Grant. We'll see about this peace business.'

"The duty was discharged only too gladly by the energetic and far-sighted Secretary; with what effect and renown the country knows full well."

The question is whether or not the story is true. I could not find any mention of this particular topic in Professor Michael Burlingame's masterpiece work, Abraham Lincoln: A Life Vol. Two.

The source of the story is Six Months at the White House by F. B. Carpenter (1879) at pages 264-267.  

F. B. Carpenter cites the publication Boston Common wealth as the source.

History is history, but only if it is the truth. But unacceptable is important lost history.

[David Lockmiller]

THE PAPERS AND WRITINGS OF ABRAHAM LINCOLN
VOLUME SEVEN
CONSTITUTIONAL EDITION
Edited by Arthur Brooks Lapsley
 
TELEGRAM FROM SECRETARY STANTON TO GENERAL GRANT.
WASHINGTON, March 3, 1865. 12 PM.
LIEUTENANT-GENERAL GRANT:
The President directs me to say to you that he wishes you to have no conference with General Lee unless it be for the capitulation of General Lee's army, or on some minor and purely military matter. He instructs me to say that you are not to decide, discuss, or confer upon any political question. Such questions the President holds in his own hands, and will submit them to no military conferences or conventions. Meantime you are to press to the utmost your military advantages.
EDWIN M. STANTON, Secretary of War.

[RJNorton]

David, I have always considered F. B. Carpenter to be a reliable source; it looks to me like he was historically correct with this account in his book.

[Gene C]

That makes sense to me considering Stanton's reaction to Sherman's terms and condition for Johnson' surrender at the end of the war. 
Stanton took  Sherman as overstepping his authority

"Sherman believed that the terms that he had agreed to were consistent with the views that Lincoln had expressed at City Point, and that they offered the best way to prevent Johnston from ordering his men to go into the wilderness and conduct a destructive guerrilla campaign. However, Sherman had proceeded without authority from Grant, the newly installed President Andrew Johnson, or the Cabinet. The assassination of Lincoln had caused the political climate in Washington to turn against the prospect of a rapid reconciliation with the defeated Confederates, and the Johnson administration rejected Sherman's terms. Grant may have had to intervene to save Sherman from dismissal for having overstepped his authority.[162] The U.S. Secretary of War, Edwin M. Stanton, leaked Sherman's memorandum to The New York Times, intimating that Sherman might have been bribed to allow Davis to escape capture by the Union troops.[163] This precipitated a deep and long-lasting enmity between Sherman and Stanton, and it intensified Sherman's disdain for politicians."
(Wikipedia)

[David Lockmiller]

David, I have always considered F. B. Carpenter to be a reliable source; it looks to me like he was historically correct with this account in his book.

I am glad to know that information regarding F. B. Carpenter to be a reliable source , Roger. There is another good story regarding President Lincoln's sense of justice in the book at page 259, prosecutorial misconduct in the case  of Franklin W. Smith.

[David Lockmiller]

The celebrated case of Franklin W. Smith and brother, was one of those which most largely helped to bring military tribunals into public contempt. Those two gentlemen were arrested and kept in confinement, their papers seized, their business destroyed, their reputation damaged, and a naval court-martial, “organized to convict,” pursued them unrelentingly till a wiser and juster hand arrested the malice of their persecutors. It is known that President Lincoln, after full investigation of the case, annulled the whole proceedings, but it is remarkable that the actual record of his decision could never be obtained from the Navy Department. An exact copy being withheld, the following was presented to the Boston Board of Trade as being very nearly the words of the late President:—

“Whereas, Franklin W. Smith had transactions with the Navy Department to the amount of one million and a quarter of a million of dollars; and whereas, he had the chance to steal a quarter of a million, and was only charged with stealing twenty-two hundred dollars—and the question now is about his stealing a hundred—I don’t believe he stole anything at all. Therefore, the record and findings are disapproved—declared null and void, and the defendants are fully discharged.”

Six Months at the White House, 259-260

“It would be difficult,” says the New York “Tribune,” “to sum up the rights and wrongs of the business more briefly than that, or to find a paragraph more characteristically and unmistakably Mr. Lincoln’s.”

[David Lockmiller]

Being informed of the death of John Morgan, [President Lincoln] said: “Well, I wouldn’t crow over anybody’s death; but I can take this as resignedly as any dispensation of Providence.”  Six Months at the White House, 259.

[David Lockmiller]

In 1863, Colonel McKaye, of New York, with Robert Dale Owen and one or two other gentlemen, were associated as a committee to investigate the condition of the freedmen on the coast of North Carolina. Upon their return from Hilton Head they reported to the President; and in the course of the interview Colonel McKaye related the following incident.

He had been speaking of the ideas of power entertained by these people. He said they had an idea of God, as the Almighty, and they had realized in their former condition the power of their masters. Up to the time of the arrival among them of the Union forces, they had no knowledge of any other power. Their masters fled upon the approach of our soldiers, and this gave the slaves a conception of a power greater than that exercised by them. This power they called “Massa Linkum.”

Colonel McKaye said that their place of worship was a large building which they called “the praise house;” and the leader of the meeting, a venerable black man, was known as “the praise man.” On a certain day, when there was quite a large gathering of the people, considerable confusion was created by different persons attempting to tell who and what “Massa Linkum” was. In the midst of the excitement the white-headed leader commanded silence. “Brederin,” said he, “you don’t know nosen’ what you’se talkin’ ’bout. Now, you just listen to me. Massa Linkum, he eberywhar. He know eberyting.” Then, solemnly looking up, he added,—“He walk de earf like de Lord!”

Colonel McKaye told me that Mr. Lincoln seemed much affected by this account. He did not smile, as another man might have done, but got up from his chair, and walked in silence two or three times across the floor. As he resumed his seat, he said, very impressively: “It is a momentous thing to be the instrument, under Providence, of the liberation of a race.”