IIRC, the bastion list lets you reserve in: hades, murder, carnage, devastation, maybe another. However, no options/upgrades may be taken for those ships (ie the full lancer murder).
limiting which IN ships a chaos fleet could reserve would work quite well. I'd say offhand: Lunar (no NC upgrade), Gothic, Dictator, Dauntless, and perhaps Armageddon.
Ray, good call on the nid, bot, elf thing. nid ships are alive and cannot be crewed - and they would just eat a hulk they captured. bot ships would be sent to mars to study. Eldar would be too proud to use other captured vessels, but perhaps tau/In/chaos could work out a way to fly those solar winds.