The Prime Directive has a dual meaning in Trek. One is prohibiting the interference with non-warp capable species. The other is not interfering with the internal affairs of another race.
So technically the Prophet/Paigh Wraith conflict would be a civil war and strictly an internal affair. Though by season 7, Sisko was pretty much putting higher priority on his role as Emissary over his role as a Starfleet officer, so even if anyone called him on it, I doubt he'd not have gotten involved.