Your mistake here is equating "wrong" with "Criminal".If Worf was in the wrong wouldn't that mean even if it had been the real BoP he destroyed he still would have been court-martialed? Since the real crime was apparently firing on a ship he hadn't identified doesn't that mean that any attack on a ship while cloaked should be a violation of Star Fleet policy? Was Kirk wrong in ST:TUC when he armed the missile to destroy the cloaked ship off the off chance that there was another cloak ship in the area that the missile might have hit?
I'd say Worf was in the wrong.
If this was a warzone with little change of civilians being around then perhaps you can say it was a sound military tactic but this didn't happen in a warzone. He was helping aid a bunch of civilians who are nearby and there was a fair possibility that the transport ship would be involved as the Klingons were attacking it consistently.
I wouldn't say it's an "off chance" the ship appeared as Worf knew there were civilian transports in the area.
Sisko is right to rip Worf a new one at the end of the episode.
The chance of the cloak malfunctioning at that exact time without the cloaked ship being hit by weapons (which would show up on everyone's sensors) is infinitesimal.
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