Yes, that is the idea. Treat all citizens in rebellious states as if they were loyal citizens, including catching and returning runaway slaves.
Whatever any of the US generals thought, that wasn't possible for US commanders after August, 1861 certainly. Under the authority of a July, 1861 act of Congress, President Lincoln declared on August 16, 1861 that all of the inhabitants of the Southern States (except for some stated exceptions) were in insurrection against the laws of the Union. We might call it the "Insurrection Proclamation."
"Now, therefore, I, Abraham Lincoln, President of the United States, in pursuance of an act of Congress approved July 13, 1861, do hereby declare that
the inhabitants of the said States of Georgia, South Carolina, Virginia, North Carolina, Tennessee, Alabama, Louisiana, Texas, Arkansas, Mississippi, and Florida (except the inhabitants of that part of the State of Virginia lying west of the Alleghany Mountains and of such other parts of that State and the other States hereinbefore named as may maintain a loyal adhesion to the Union and the Constitution or may be from time to time occupied and controlled by forces of the United States engaged in the dispersion of said insurgents)
are in a state of insurrection against the United States, and that all commercial intercourse between the same and the inhabitants thereof, with the exceptions aforesaid, and the citizens of other States and other parts of the United States is unlawful, and will remain unlawful until such insurrection shall cease or has been suppressed; that all goods and chattels, wares and merchandise, coming from any of said States, with the exceptions aforesaid, into other parts of the United States without the special license and permission of the President, through the Secretary of the Treasury, or proceeding to any of said States, with the exceptions aforesaid, by land or water, together with the vessel or vehicle conveying the same or conveying persons to or from said States, with said exceptions, will be forfeited to the United States; and that from and after fifteen days from the issuing of this proclamation all ships and vessels belonging in whole or in part to any citizen or inhabitant of any of said States, with said exceptions, found at sea or in any port of the United States will be forfeited to the United States; and I hereby enjoin upon all district attorneys, marshals, and officers of the revenue and of the military and naval forces of the United States to be vigilant in the execution of said act and in the enforcement of the penalties and forfeitures imposed or declared by it, leaving any party who may think himself aggrieved thereby to his application to the Secretary of the Treasury for the remission of any penalty or forfeiture, which the said Secretary is authorized by law to grant if in his judgment the special circumstances of any case shall require such remission..."
Done at the city of Washington, this 16th day of August, A.D. 1861, and of the Independence of the United States the eighty-sixth.
ABRAHAM LINCOLN."
Gen. Butler inquired in May, 1861 about slaves running away to the US forces. The Secretary of War subsequently instructed Butler to do nothing contrary to the laws of any State in terms of carrying off or liberating slaves, but where slaves came to the US forces themselves, to not presume to return them to masters in States subject to the Confederate authorities:
More certain authority for the liberation of slaves was established by law on July 17, 1862, which declared that the U.S. Government, through the civil courts, had the power, relative to citizens in insurrection and rebellion to convict and punish with the confiscation of property including slaves...
Also, from the same act, relative to the armies, any slave in the Confederacy who were thereafter either captured by, or ran away to US forces, were free in spite of any State laws to the contrary, and any US military officers who presumed the validity of the claims of slaveowners within the Confederacy would forfeit their commissions...
President Lincoln's emancipation proclamation was a public notice relative to the general enforcement of this act, per his war powers.