I think the situations in Season 6 and Rough Beasts are different. Sisko's actions in Rough Beasts are not consistent with Sisko's character based on the Season 6 opener. In Season 6, Sisko left the station because he was grieving over Dax's death. He didn't abandon Kasidy then. He went home. I think its something she would've understood even if we didn't get to see a scene with them discussing it. Further, I didn't see anything in that episode that would've prevented Kasidy from joining him. In Rough Beasts, he leaves her behind without explanation and then files for divorce. He is purposely cutting her out of his life in Rough Beasts and he didn't do that from what we saw in the Season 6 opener.
And I do think that once you marry that is another level of commitment, plus in Season 6 no small child was involved. At the start of Season 6, though Ben and Kasidy had been together for several years they had not taken that step. And Ben took that step in defiance of the Prophets, so it seemed inconsistent that he would not be defiant in this instance, especially without out clear proof that the prophecy of doom will impact his wife and child.
I might be wrong but I got the feeling that Sisko also speculated that the shroud around him had also something to do with his father's death as well, and if that's the case it's possible that DRG III's Sisko is an irrational paranoiac who believes that death will come for anyone close to him. That's what I was aiming at when I wrote that Sisko was potentially toxic and a threat. And I don't recall the Prophets spelling out much of anything in Rough Beasts, just Sisko's speculation of what he thought they meant, so I'm not so certain about how clear things were as you are.
I am not accusing DRG III of purposely going against Avery Brooks. I can't see a reason why he would do such a thing and I'm not inside the man's head. But from what I've seen of Sisko on screen and in many novels and comics, I do believe that DRG III's take on the man is not one I agree with and does not seem consistent with what has come before. I can understand the need to inject drama and tension, but I think it could've been handled in a different way and one that actually made Kasidy more of an active participant than a victim of Sisko's seeming capriciousness.
Though for the sake of argument it wouldn't be the first time that Trek Lit. overturned a decision made on a TV show (Trip on Enterprise) for example. But once again, I'm not accusing DRG III of that. Perhaps he was just trying to make good on the Prophets' threat from the show. I didn't like the way he did it.
As for the hostile environment on the Trek boards, I think using terms like 'throwing a hissy fit' is negative. Even in the Rough Beasts forum you had supporters and detractors, but I would argue, as a detractor, that a lot of the disappointment came from our love of the character of Sisko, and I, for one, didn't like what I saw happening to him. Family had been a big part of his character and I saw that being ripped away from him and I didn't like what DRG III was replacing it with, a craven, morose man on a bland starship.