When you join a military or paramilitary organization, you agree to abide by the rules of conduct in that organization. Worf clearly violated those rules, even if that violation was still within the boundary of his personal cultural belief system.
Again: HOW did Worf violate Starfleet regs?
In all three of these instances, Worf did not challenge a fellow Starfleet officer or Federation citizen. If he'd done that, I could understand why Starfleet would be concerned, because Starfleet crewmembers just don't duel each other whenever they feel like it. But that's not the issue here. Worf's opponents were all Klingons. Starfleet and the Federation were completely irrelevant in all of these examples. ALL of them were internal Klingon matters. (Remember, Worf does not stop being a Klingon just because he has joined Starfleet.)
I'm fairly certain it's against Starfleet policy to murder foreign dignitaries or stand by and do nothing during same. Otherwise the crew wouldn't have been too worried about Geordi trying vaporize Vagh in "The Mind's Eye" nor would Riker have felt all that compelled to stop Yuta from assassinating Soveriegn Marouk in "The Vengeance Factor."
Indeed, it would be a violation of the Prime Directive for the Federation to interfere...
Not if the person committing the crime wears a Starfleet officer. Worf killing Duras could easily have been viewed by many in the Klingon Empire as Starfleet interfering, even if Picard hadn't sent Riker over to try to stop Worf. Why? Because (aside from Worf literally wearing his Starfleet uniform at the time) Worf was also --wait for it-- a member of Starfleet.