I'm suddenly reminded of the EQ1 reputation grinds some people went through (myself included) to be able to get into certain cities as certain races (Iksar going anywhere? yeah that took awhile). Not saying that's the way to go for TOR (I personally despise reputation grinds nowadays, especially when they're used to gate players from content and gear) but given TOR's story-based nature I don't see why some sort of "grey market" or "enemy of my enemy" shindigs can't be worked out.
Especially with the premise of a faction rising to challenge both the Empire and the Republic.And no, I'm not advocating for defections.