When I was younger I think I leant more towards Bashir's blind optimism. I was also a bit naive in thinking that I wanted him to find the cure by the end of the episode, which would have robbed it of any emotional resonance. Nowadays I totally see where O'Brien was coming from, but I only think he was right because of the messy situation they were in. I would still lean towards supporting Bashir finding a cure after he returned to the station, although mostly because it would have been an interesting development for the Jem'Hadar not be dependent on the Ketrecel White.
I quite liked Indiscrtion, but I probably agree that it lost its way as it went on. I just love that natural enemies Kira and Dukat have to work together - it provided a brilliant opportunity for the two to discuss things, which was pretty riveting. And Dukat getting a thorn up his arse was hilarious!