Because they had been at war and had to show they were no longer at war but were peacefully part of the union
It's as if they said in 1861 that the South was not allowed to leave; but in 1865, they said, until they passed certain laws, they would not be let back in. The positions are contradictory, though they are expedient political rationalizations. In both cases, they retain for the federal government leverage that they really shouldn't have.