Reminder that in both cases Sisko 'crosses a line' and starts in on a scheme to do some morally questionable shit, he informs Starfleet and Starfleet belatedly gives him permission.

>Oh you want to poison an entire planet settled Federation citizens because they did the same to the Cardassians? Sure, go ahead
>Oh you want to find some "evidence" to bring the Romulans into the war against the Dominion on our side? Sure, go ahead
Hard to call him a hypocrite when he explicitly gets the go ahead from his own superiors. Even when he's pushing boundaries he's still doing it within the framework of what Starfleet considers acceptable behaviour.