As to the original question, An admiral straight out tells Sisko that interfering with the Bajoreans request to Leave DS9 was a violation of the Prime Directive. Also taking sides on the coup is a violation of the prime directive. Sisko argues that it's not internal, because the Cardassians are behind the scenes, but the admiral is quite clear, that just because teh Cardassians are willing to interfer doesn't give him the right to.
Now of course Sisko tries to side step this, by saying he is leaving slowing. Utter bullocks. And he has Kira present the evidence again Jaro. But its only due to Federation assistance. Federation transport to the Bajorean moon, Federation technical support to get the small fighter operational. And of course every single moment, let alone actively fighting against the forces, sabotaging the systems, ect are all violations of the Prime Directive.
Th episode the siege as per episode probably some of the largest number of acts that are violations.