Something I love about The Way of Warrior
is that Sisko is completely willing to tell Starfleet Command to go to hell.
Here's another example of the Prime Directive being used to avoid any responsibility. Federation security is at stake, but TPTB want to let the Klingons attack because it's "purely an internal matter."
You can't sit by and do nothing when an atrocity is about to be committed. You don't let a race get exterminated, even if that race is the Cardassians. Sisko continues doing the right thing to keep the Alpha Quadrant strong enough to resist the Dominion.