The idea of choosing who to save is interesting. I'd be careful how many of those get thrown in though; the more combinations there are, the more branches you have to write out. And it will probably branch a lot if you're doing it early in the game as you say, unless you're only offing minor characters whose presence in story events is basically interchangable with the other person who could've been there at the time.
If the characters you have to choose between can actually play an important role in the story, one thing you might consider is making the major story branches based on who survives.
