Wanting to run away and actually doing it are two different things. In season 6, Ben and Kasidy were not married, nor did they have Rebecca. And it must be noted that Sisko left the station to go back home, to his father, and he brought Jake along. So Sisko left the station true, but he 'ran' back to his family.
In Rough Beasts, not only does he abandon his wife and child, he also abandons Jake and the rest of his family. He leaves them to deal with his father's funeral, which is something that doesn't gibe with Sisko based on how close he and his father were on the show.
Leaving Kasidy bothered me, but also how it was done. He couldn't talk to her about it? I don't think what DRG III did was consistent with the character, no matter what the interpretation. He completely cut Kasidy out of the equation and left some good character work/development on the shelf.
And if he's so potentially dangerous now, so toxic, why go to a starship with hundreds of people on board? Why not just get a ship and travel around yourself or become a hermit somewhere?
And with stereotypes the fine particulars are not looked at. People will look at the surface. Is he with his family or not? Did he leave his family or not? And Sisko left his family. Now, I don't think I would've liked this outcome however DRG III did it because it went so against how Avery Brooks and the show developed Sisko's character, but at least I might have understood it better if he had written some scenes between Sisko and Kasidy where they talked about his decision.
But overall Rough Beasts was a mess, two novels in one, thrown awkwardly together, and a story of this magnitude (same with Spock's) deserved a full novel of its own to delve into all of those issues.