Y'know. That bit about "the problem is people pirating in cruisers" really struck me.
This entire time the mod seems to have been geared around a fantasy world in which the most advanced military in Sirius has the same quality of equipment as the most rag-tag pirate faction.
If lawfuls are allowed to destroy transports and such in capital ships, and pirates and unlawfuls aren't (in space that doesn't belong to them at least) then it would actually bring a bit of balance to the issue. Battleships dot the houses left and right, along with cruiser patrols and the like. There's no reason why a cruiser captain should have to sit back and watch people die just because of some arbitrary rule that wasn't even intended for his circumstances.
Besides, if somebody posts the "abuse" card then I'd ask you: what does it matter when you already, and always will have, lolwuts blowing up random stuff in capital ships anyway? So they'll romp around for a bit and get sanctioned, end of story. It doesn't warrant a BS rule that results in the situation described here.
"Oh I'm sorry, it's a waste of resources. Sorry about your three-thousand passengers, maybe a rescue ship will show up."