I don't agree with the "other guys are doing it" argument. Davis and the CSA government had its faults, no doubt, but that is no excuse for Lincoln to disregard habeus corpus and the US Constitution. Disregarding habeus corpus during a rebellion is Constitutional (see Art. I, Sect. 9), and any argument that Congress alone had that power is defeated by their firm appoval of Lincoln's action.
What of Chief Justice Taney's ruling in Ex-Parte Merryman (1861)?
Taney ruled against Lincoln's suspension of habeus corpus.