Lincoln ordered Frémont not to shoot any prisoners without his (the president's) authorization. Lincoln feared that Frémont's threat that "all persons who shall be taken with arms in their hands within these lines shall be tried by court-martial, and, if found guilty, will be shot" would lead to the Confederates executing any prisoners they had taken in retaliation.
Lincoln did not order, but strongly suggested that Frémont modify his emancipation proclamation. In his letter, Lincoln said that he believed the proclamation "will alarm our Southern Union friends and turn them against us; perhaps ruin our rather fair prospect for Kentucky."
Kentucky, with its divided population, was still pursuing a policy of neutrality, and both sides were still tip-toeing around that neutrality, recruiting, arming and training men from the state, but avoiding overt acts that might push the state toward the opposing side. Lincoln feared that making the war about slavery would be just the thing to push Kentucky into the Confederacy.
Lincoln also feared that this proclamation would have an adverse affect on the slave states that were still in the Union and the Northern Democrats who were helping to fight the war.
On August 6, Lincoln had signed a confiscation act into law. This act, which passed the House 60-48 and the Senate 24-11, permitted the confiscation of any property, including slaves, that was used to support the Confederacy. The act stripped owners of their slaves, but left the status of the slaves unresolved. For the time being, they would be the property of the Federal government. Lincoln suggested that Frémont modify his proclamation to conform to the confiscation act.
Lincoln's letter to Frémont:
WASHINGTON, D.C., SEPTEMBER 2, 1861
MY DEAR SIR:--Two points in your proclamation of August 30 give me some anxiety.
First. Should you shoot a man, according to the proclamation, the Confederates would very certainly shoot our best men in their hands in retaliation; and so, man for man, indefinitely. It is, therefore, my order that you allow no man to be shot under the proclamation without first having my approbation or consent.
Second. I think there is great danger that the closing paragraph, in relation to the confiscation of property and the liberating slaves of traitorous owners, will alarm our Southern Union friends and turn them against us; perhaps ruin our rather fair prospect for Kentucky. Allow me, therefore, to ask that you will, as of your own motion, modify that paragraph so as to conform to the first and fourth sections of the act of Congress entitled "An act to confiscate property used for insurrectionary purposes," approved August 6, 1861, and a copy of which act I herewith send you.
This letter is written in a spirit of caution, and not of censure. I send it by special messenger, in order that it may certainly and speedily reach you.
Yours very truly,