Actually, I've found that what people want is almost NEVER "for the best." Funny how that works.... either we're all functionally retarded or we're just a bunch of masochists.
At this point, its probably best if she doesn't pick you. Now that you know the doubts she's having... well, even if she chose to be with you those doubts would still be there. Stuff like that can poison a relationship. Its a sucky situation, but its my duty as your friend to put that nugget of wisdom out there.
She's probably making the right decision if that's the case. I mean, long distance relationships are hell, to put things mildly. Even when they work out, its a whole lotta heartbreak. But hey, maybe she'll decide to take the chance.