Yep. The key to understanding Aeon Flux is to grasp that the war between Monica and Bregna absolutely does not matter one little bit: it's a pretext by which two perverts explore their sexual fascination with one another and play endless games of sadomasochistic one-upmanship. It's a kinky Spy Vs. Spy, a satire of Star Wars-like SFF morality plays; trying to actually make the Monica-Bregna thing important just turns AF into that which it's satirizing.

(And don't even get me started on turning Trevor into an unambiguous good guy, because Jesus Christ.)