I recently binge-watched a show in which the protagonists discover that what seemed to be a single mysterious enemy organization was actually two diametrically opposed factions. When trapped by one faction, they were able to draw in the other one and escape in the ensuing chaos. It's an idea that's not actually uncommon in non-interactive media, and RTS games will also sometimes have 3+ sided battles, but I think it could work for RPGs as well.
There was a thread recently about keeping the enemies in the first Pillars of Eternity game low-level. This approach is probably the most sensible