Why would it be odd? He was clearly uncomfortable with the decision he made, and even with the whole "I think I can live with it" statement his body language betrays a lack of confidence in the moral imperative he felt.I think facing what was coming, the Sisko had a moral imperative to do whatever it took to defeat the Dominion by any means necessary. but that he became squeamish about Sec31 doing the same thing (successfully) later, seemed a bit odd.
To be faced with a similar situation would be just as uncomfortable as before.