My solution for the issue is simply to leave the creature threesomes enabled, but if I get knocked down in one of the rare situations where there are more than one allied creature race present I disable it in the MCM menu on the fly.  If I know I'll be adventuring in a place like that for a longer time I'll leave it off until I'm done - this usually means Falmer for me as in my game I'm often fighting Falmer, human females (Forgotten Wenches), and both types of chaurus, and sometimes modded chau