maybe she was already dead - and the Prophets kept her alive to meet their needs?
I don't know about the Prophets, but the Pah-Wraiths were definitely shown to be able to take over living bodies (Keiko, Dukat), so there would have been no reason to take over a dead one. Plus, if Sisko's mother was already dead, you'd think that she's go back to being dead once the Prophet left her body after Sisko was born. That didn't happen.
I'm afraid I have to agree with whoever said that the Prophets pretty much used this person against their will. And the worst part of it is that Sisko never even brought that up. If I found out that the person I thought was my mother really wasn't, and that my "real" mother was some stranger possessed by some alien in order to create me, and never actually loved my father or even gave a shit about him, and then left him once she realized what happened, I'd be highly pissed off. It was just some nuttiness that came out of nowhere and wasn't handled in the most realistic of ways.