Yup, the Emancipation Proclamation only applied to “the states now in rebellion” and it only freed slaves in the Confederate-controlled states and not in any place the Union controlled. One of the few accurate statements you have made.
If that is so, Lincoln was guilty of violently overthrowing the constitution of the United States. Slavery was enshrined in the constitution thanks to the attitudes and actions of the northern states during ratification.
But the Confiscation Acts of 1861 and 1862 gave the government the power to seize private property without compensation if that property was used to the benefit of the Southern rebellion. Slaves were certainly used for that, so Lincoln's proclamation was not only legal it was Constitutional. See 1863 Supreme Court decision in the Prize Cases (67 US 635).
Lincoln could have attempted to peacefully amend the constitution to end slavery but he chose war.
Lincoln did peacefully amend the Constitution to end slavery, once the war that the South forced upon him reached a point than enabled him to do so.
“But the Confiscation Acts of 1861 and 1862 gave the government the power to seize private property without compensation if that property was used to the benefit of the Southern rebellion.”
See U.S. constitution, Amendment V . . . “nor shall private property be taken for public use, without just compensation.”
Of course, by that time, the north had already taken up arms to overthrow the U.S. constitution.
Once Cain decided to slay Able, what was one more violation of the constitutional covenants?