I echo the point, civil wars only happen for native MFs so they can't be retreated. Did you mean War?
A good (slightly longer!) way to force a retreat is allow the target MF to win a starport/outpost (assuming the system has more than one) and if the station has a black market then that can be used to hold the MF's head under water. And once retreated, any assets (i.e. stations) pass across to the strongest MF in the system.
Regarding boosting other factions, I often aim for the leading MF to be between 55-65% and the second place 25-35%, so the totals range 80-100% (the latter impossible unless a two-MF system) and this should force any other MFs to single digits (and may avoid any of the smaller MFs getting into Conflicts of their own). To me this is a more stable approach to system management, rather than having other factions all jostling in the 10-40% range and triggering conflicts willy nilly.