At low stability when a civ breaks away from an empire it could start out as a vassal to the empire it broke away from.
If a civ breaks away from a human players empire the could be a pop up asking whether to grant them full autonomy (not a vassal, and at peace, huge diplo bonus), limited autonomy (vassal state) or declare war.
Secondly for the civil war, if it is the human player who goes into civil war how about spliting the empire into 2 halves with the human player controlling one half and a single independant civ gaining the full second half?
This would make reconquoring your empire not only possible but also quite fun? Also for a very large empire it could be split into 3 blocks as the are two independant civs.