The answer to what I think was your fundamental question is that it should not be a problem, as long as she has both her passport and her marriage certificate, to fly. We were in the same situation shortly after I got married - my wife's ticket was in her new surname, but her passport was still old. Marriage license shown, no problem.

That being said, this all took place prior to 9/11. I'd suggest calling the airline directly to determine what their ID requirements are. If this is not to be an instant honeymoon (i.e. if they're leaving more than 3 days after the wedding), there should be no problem taking the marriage certificate to the nearest passport office and getting a same-day name change on the passport. That would certainly make travelling much easier.