Some of the events that occur during the events of Operation Raccoon City are considered non-canon to the series. Obviously, given the fact that it is set around the same time as Resident Evil 2 and Resident Evil 3, it wouldn't make sense if Leon died, because we all know that he has since gone onto become the main protagonist of Resident Evil 4, and has been confirmed as a playable character for Resident Evil 6.
Presumably, if we are given the choice of killing off poor mop-headed Leon, it'll just be for the sake of playing out a 'what-if'-type scenario.
Here's to hoping that we can murderize Claire, too.