Talking of Sisko's behaviour, I just re-read Fearfull Symetry and The Soulkey, and both novels already start Sisko on his new path. He is appereantly given a vision by the Prophets of things to come, atleast that how it is comes across to me. And judging from what we know, it was probably a vision of the Trouble with the Ascendents.
What he did to Vaughn, I feel, was horrible but nessecary. If Vaughn hadn't taken out his counterpart, both and Opaka would have tried to save his counterpart, meaning Opaka would probably be killed during the Klingon's raid. Opaka is appereantly needed so the Bajoran's in the Mirror Universe can finally achieve the spiritual mindset that is needed. I kept getting the feeling that the entire situation with the Ascendents was going to involve the Mirror Universe as well, or perhaps the entire Multiverse, since the Prophets found it nessecary to have The Sisko be the Emissary in every Universe, not just ours.
Sisko, at that time, felt the actions towards Vaughn were justified, since it was all for Them. So, if anyone wants to blame anyone for Sisko's path, please realize that it was all part of a bigger plan for the DS9 story arc already laid out, one that ultimatly never came to fruition.