I asked this very question several months ago, and got some answers from /u/ReadySettGo and /u/rittermeister, among others.

The short version is that such actions were practically unthinkable at the time, as they would have compromised a fragile peace and made any sort of political reconciliation impossible. By and large, the Union leadership wanted to re-integrate the South into it's political structure as expediently as possible, not give the Southern ownership class even more reasons to support future armed rebellion against the Federal government.