He couldn't. He didn't have the same authority to do so in non-rebellious areas, as his CinC powers gave him in areas under armed insurrection and subject to martial law. To universally outlaw slavery took the 13th A.
Actually his powers as CinC were not applicable - the US Supreme Court had previously held that uncompensated actions were illegal. After the war, that Supreme Court held 9-0 that the Constitution is for rulers and civilians, in war and peace.