Why should they always be treated as the enemy? Part of the fun of Mork Borg is that everything is doomed, and your character is scum. You can be a piece of shit if you want to. The role-play is completely open; it's not hampered like D&D where you literally just can't be evil.
Not to get too bogged down in knee-jerk reactionism, but my thinking was that there's a difference between being a "fun piece of shit" and being a militant fascist (Inquisition) or eugenicist (Mendelite). I will also admit that perhaps they don't read as blatantly aligned to those real-world ideologies as I meant when I first wrote the factions.