Personally, I would mind neither option 2 nor 3. I can see how others would be rather pissed if they have to get rid of/change factions with some of their chars, though.
I totally agree with Tank on that matter: If people can't separate their different factions' chars, it's their problem. Just shows that they can't stay within RP. So option 3 shouldn't be necessary.
As for the SA/HF/SCRA battle thingy: I wasn't present on that particular occasion, but I know that the HF were neutral with the SA for quite a long time (an unstable truce). When I joined the HF, that truce was already in place. I doubt you'd break a truce without any reason. You'd rather team up against the common enemy, even if you still mistrust each other.
So, as long as they didn't party together afterwards, I think it's all within RP.
:yahoo::yahoo: