Yeah, the notion of being allied with literally everyone in a system, even the mortal enemies, seems a bit daft to me.All the more reason to not distinguish criminal and non-criminal activities for the purposes of reward, in the game design sense
Here's a thought; how about we reflect the negative impact "Lawful" actions have on other factions (through lost influence) on a commander's reputation with that faction.
Yeah, I ran dozens of massacre pirate missions and trading for a single faction and they're now in Expansion and in control of everything, but every other faction losing out hates my guts for it.
Oddly enough the FE2 military ranks worked like this. Doing work for one lowered your score with the other.