I would doubt it. First, the nuclear use policies regarding use of weapons are all designed around the idea of a coherent, unitary executive in the federal government. They are not specific to any particular "enemy" — they are about enabling the President and the Secretary of Defense to create and implement nuclear policies.

The actual "war plans," like the SIOP, are designed around specific foreign enemies in mind. Those are already complex enough; it is hard to imagine how they would develop such a thing for a hypothetical domestic enemy in a hypothetical domestic civil war, the parties of which are anything but clear.

Assuming a continuity of military power and policy, the existing frameworks probably suffice for adapting to any such situations. If one does not assume that (e.g., if one assumes the military itself is fractured by such a thing), then probably all of that is up in the air. I have never seen any indication that any official policies have ever taken this possibility seriously (for good or ill).