Please let me know of any mod that has compatibility issues. This is bound to happen, as Pacifist basically removes "everything that's a gun", "everything that is ammo", and so on. Mods that rely on their custom guns, ammo, turrets, etc. might become unusable or prevent the game from starting.
Alternatively, report broken mods here: https://github.com/Derpumu/Pacifist/issues/1