The Sisko is really not himself right now, he's back in his S1 mindset. I'm confident he'll pull himself out of it eventually.
You need to read Plagues of Night
and Raise the Dawn
Oh yeah, I did. Its been a while though. I read them when they first came out.
Probably explains why I was so sure he'd pull through.
I wanted to say he already had but I just couldn't remember.