Best idea yet that I've seen on this site. I would fully support a Department of Peace in any country of the world. However, the US and its citizens must make sure that after the creation of such a department it does not quickly disintegrate into a defunct institution paying lip service to ideals. It should be fully funded and its activities adequately and regularly publicised to the public.
The proposed amendment to your Constitution would fail, mostly because the law would not have general application to all, but only to a select few that, for political reasons, are deemed enemies of your state. This itself would be said to contradict the rule of law: everyone is not equal in the eyes of that law; and power is wielded arbitrarily.
In essence, the state has committed a crime. Although perhaps politically unpalatable, the only way to get out of the mess is to try to make amends and face the consequences of detaining civilians contrary to the rule of law in the first place.