I think it was a bit of a surprise, but I think it was simply that the voters thought she most deserved it. I don't think Kelly was seriously in the running. She'd won for a performance in a better show two years before. People probably thought she was good again, but not good enough to win again so soon in that group. My guess would be that she got the fewest votes.
As for Ryan, I seem to think I've read that she'd had a relatively minor stroke during rehearsals, but she was determined to open in the show. I think perhaps her performances were uneven after opening night because she was in poor health, and that may have been why (or part of the reason why) she didn't win, which some said is what happened with Kathleen Freeman years later (ill health leading to performance problems as the run went on).