A novel can polarize it's readership, no question. However, it can also bring them together. Writing something for the shock value needs to have a very good reason behind it.
Sisko's actions bringing the Romulans into the Dominion war were shocking and in many ways reprehensible. He may not have done the deed himself but he was satisfied with the outcome. The journey to that point was a fascinating one but there was build up to it. Sisko came down a long, torturous path that brought him to a fork in the road and we were shock, surprised and saddened when the turned left instead of right. We may not have agreed or approved of his decision but we could understand why he did.
Due to the gap in DS9-R, we didn't see the path he took to get to that point. We were told what he did and why he did it. That may be satisfying enough for you, you. You seem to be more interested in where he goes from here. For me, it felt hollow. I'd much rather see the journey that took him to that point and see for myself what he went through in making the decisions that he did. Of course I'm interested in where he goes from here but, seeing as I know what happens, filling in the backstory at this point seems a little pointless. I'm sure that a lot of our questions will be answered but it's just to get us up to the point that we already know where he is.
Some more good points. I don't know if I would ever like the decision to leave his family behind, however if we had seen the evolution/devolution of his thoughts more instead, instead of doing this time jump, I might have been better able to understand Sisko did what he did. I think the time jump and the structure of Rough Beasts itself also didn't help. There were two, maybe three, stories awkward put together in one novel and none of the main characters really got the exploration they deserved.