It's never going to possible since you'd have to the voice overs for quests on both factions. What they could do instead is add more dialogue options with characters of the other faction you come across (along the lines of the stuff you talk about with Ardun Kothe as an agent or the stuff that line with the imperial scientist on balmorra that you meet as a SI). You know, stuff that *hints* at defection or working undercover, stuff like that.
It could be really interesting if done right. I mean, just look at how oftne the agent story is praised just because of little stuff like that.
And I don't mean go back and change old quests. I mean for future expansions and stuff. I think it could be a major draw for people to play certain classes.