The Supreme Court had already established the legality of the Confiscation Acts which allowed the government to seize without compensation private property if it was used to further the cause of the rebellion. The Emanicpation Proclamation can be seen as a continuation of that. Slaves were used in support of the rebellion, freeing them in those states in rebellion was a valid tool to be used against the southern war effort.
PRIOR to the war the Supreme Court had ruled that uncompensated takings were unconstitutional. See the 5th Amendment.