Hey, every Starfleet captain has broken the PD at some point. Personally it makes me mad when they quote the PD as a justification to let some ecological disaster kill an entire people. Just because I'm listing violations doesn't mean I think they're not justifiable.
1) As far as season 1 eps go, Captive Pursuit is pretty good. Interesting dilemma and culture.
2) Bell... well technically he is interfering with Earth's past, even if he's trying to restore it. I did love the follow up in Little Green Men when Nog comments on Bell looking like Sisko and Quark going "all hew-mons look alike."
3) ITPM is a violation undoubtedly. Justifiable? Sure. He did get approval after all. As for Worf killing Gowron... this is from Tacking Into the Wind:
SISKO Something has to be done.
WORF I agree. And I have a solution. But it will not be easy.
SISKO Do whatever it takes, Worf. Those Klingon ships out there are the only thing between us and the Breen. Gowron's risking the safety of the entire Alpha Quadrant and it has to stop.
Next scene he's in Worf kills the Klingon Head of Government.
4) Starfleet never did like Sisko doing this, but put up with it probably because it'd make the Bajorans mad.