The whole Prophet thing wasn't a violation because at the beginning he discouraged it, and he didn't do anything to encourage it until later on when Bajor was effectively an ally of the Federation.
The Tosk thing is not a violation because it was the other culture who chose to come onto their station, not the other way around. Also you could argue it was a form of asylum.
The whole ITPM thing was an ethical violation, arguably a justified one, but not a violation of the prime directive. The Dominion War was not an internal Romulan matter. The Romulans were already involved in the war. They involved themselves in The Die Is Cast and even showed up to defend the station once before when they thought the Dominion was invading. That situation was strictly an 'ends justify the means' question.