I think sneezing counts as a Prime Directive violation in some cases. So pretty much everyone in Trek who goes to another planet has probably violated it in some way.
I think in the basic
sense of the Prime Directive (interference in the development of a pre-warp society), though, Sisko hasn't. But in the broader
sense of the Prime Directive (involvement with other civilizations period), Starfleet violates the Prime Directive every time it contacts and interacts with other non-Federation races (such as the Bajorans).