If you are wanted, the wages of sin is death; that's how the game works. It doesn't matter if the rest of your passengers are not wanted. In much the same way that it only takes one ship being attacked (not the entire instances) to trigger a crime. Context here is meaningless; at least, it always is, when the "stronger punishment for crime" skeleton is given the occasional shake? Maybe it
is actually a little complicated; so maybe some considered thought is required?
Yes, I know. Kofeyh you're being silly. Bad people should always be punished, you are quite right.
Crime is complicated; unfortunately the game, and the AI, cannot really consider context. Merely one's state. If one is wanted, that's it. Lights out. Yes - a warning would be wise; but then one can simply abandon the mission in the time the warning is given, and effectively avoid consequence. So is that really to be encouraged? How do you induce risk without trivial absolvement?
Perhaps the mission description should carry a warning if there's additional risk to the commander; people can then make an informed decision. But I'm not sure Frontier necessarily wants to telegraph risk to commanders in all instances.
So perhaps it's a case of there being strong penalties for ditching a wanted passenger (you are, after all, aiding and abetting a wanted criminal) and tag the mission with a (apparently much clearer) warning of hostile actions. That'd strike me as a more reasonable outcome.
edit: the suggestion of handing over a perp after they become wanted is interesting, but why have criminals at all, as a risk vs reward mission, if you can trivially ditch them (either out the airlock, or dump them at the local constabulary). I think it's much more interesting that the commander is faced with an
actual dilemma.