It was unconstitutional for Lincoln to free them in any state that was part of the Union, rebellion or not. It is in fact a denial of due process to simply declare every citizen of a state to be in "rebellion". If you actually look at the votes for secession, it was just a majority, and that leaves millions of people against it.
There was no "except for rebellion clause" in article IV, section 2. So long as a state was part of the United States, Article IV, section 2 should have been enforced.
Lincoln's position was that no state had left the Union, therefore they were all entitled to the same constitutional protections as the other states.
Lincoln had the constitutional authority to declare slaves “contraband of war” in states that were in rebellion.
No he didn't. It wasn't a "war." According to Lincoln it was a "rebellion". A "war" is fought against a foreign power which is not entitled to Constitutional rights. Anything seized from a foreign power is fair game, but there are actually constitutional laws that protect people who are under constitutional law.
Lincoln simply ignored these, and decreed what he wanted. He even locked up a congressman who said he was acting like a King.