Three things.
First, it's quite likely Sisko was ineligible for promotion during the Dominion War due to him being directly responsible for keeping the Bajorans from joining the Federation. (Admiral Whatley said, "I could have your commission for this." Could very well have been a formal reprimand, keeping him from moving upward in rank for a while.)
Second, Sisko was Ross' adjutant during "SACRIFICE OF ANGELS", so he had the authority. (As we've seen elsewhere, position is the deciding factor over rank.)
Third, the plan was Sisko's, so it made sense for him to be the one in charge.