Well, there are the higher costs and all the scheduling with potential voice actors and such. I am not saying they shouldn't do something, but whether they wil I am not too sure. They can either stand by story and just claim the players need to change their perspective. (Just saw a review today, that basically stated as much, that most people may be looking at the story from a "wrong" angle). It's also bit new territory for them, so can't be sure how they handle it, I can't remember them ever being in a position like this where people were really disappointed by their storytelling and were asking for changes.
That might lead to a happier ending, but whether it is something that's written with "Eh, let's just write something that makes them happy" or something that has a lot of thought put into it remains to be seen. I don't want to be too pessimistic, but so far none of the games that I've had problems with (ME3 latest that comes to mind), have really fixed the problems. They've put on quick fixes, but end results were rarely much more satisfying than the original.
Still it'd be interesting to see their take on the ending or how they came to write these specific options, while not leaving any endings where the main character actually survives or has a ending that serves a proper purpose.
(Sorry, if I am repeating what someone else already said, haven't caught up with the thread fully yet)