The prime directive doesn't apply to other advanced spacefaring civilizations. Now the Federation has a policy of not getting involved in a star nation's internal affairs, but during a time of open warfare a lot of things go out the window.
So no, it wasn't a prime directive violation, but it was an ethical violation of principles that Sisko believed he stood for; but because of how the war with the Dominion was going, it was a personal ethical violation he could live with.
Actually, that's not correct.
The UFP PD protects less advanced civilizations yes, but its not exclusively applied to them.
The PD prevents interference into a cultural matters of other species in general (advanced or not).
In TNG, Picard had to be very careful around the idea of allowing Worf to jump back and forth between Klingon warrior and SF officer when it came to participating in events. Even Picard himself drew the line on direct interference and had to exclude himself from what was an 'internal Klingon matter'.
So, no, the PD does NOT exclude advanced spacefaring civilizations.
What Sisko did was a gross violation of PD...he turned a blind eye to a murder after allowing Garak to FABRICATE evidence which made it seem like the Dominion was plotting against the Romulans so the Romulans would join UFP and Klingons against the Dominion.
Was it the right thing to do? Probably not. Was it necessary? Maybe, maybe not. Perhaps there was another way to bring the Romulans into the fight against the Dominion, we don't know.
Point being is that like any other war crime... Sisko should have been held accountable.