I have read the book, and it actually read less like the begining of an arc and more like a part two. There were a lot of important events that happened to Sisko that shaped his outlook and decisions that were alluded to in RBoE, but not yet chronicled to us the readers (The Ascendants conflict and Rebecca's kidnapping to name two). I would be willing to believe that Sisko's actions may make more sense once we read the stories that shaped his perspective in RBoE.
This is the most logical assumption, but a lot of people seem to forget this, and think the writers decided to have Sisko act like this out of the blue. There are reasons for Sisko's behaviour, and I wouldn't be surprised if one of David R. George's books to be released in 2012 is going to deal with this. I certainly hope so.
Or it could just that part of the plot is badly written. I'm pretty sure that before he flounced off, George said that everything you needed to know was in that book.
Ofcourse everything we NEEDED to know to understand this novell was in the novell. But no complete details.
It really feels as if haters gonna hate in this topic, and lovers gonna love. It doesn't even feel like a discussion anymore. I think by now it's been established quite well that RBoE is one of those you love or you hate books. Which is ok I guess.
To me, the Sisko story works. For others, it just doesn't. I guess that's all there's too it.