Yeah, honestly I just don't know exactly what kind of work goes into it and what kind of strings they need to pull to rework current companions. I know we've discussed a lot of different ideas before, like a way to "reset" companions. In one sense I think that wouldn't be too bad of an idea since it would allow people to go through it again without leveling from scratch, but then maybe that trivializes your decisions somewhat.
I have only finished the trooper story so far, but unless the other classes are radically different, decisions you make regarding your companions are already unimportant (from the moment they join in the case of Jaesa). All that they really affect are affection. And you can raise that with gifts to negate the fallout of any decision your companions did not like.