No way Kira is dead. I mean, if she was, then what was the point of having Vaughn cling to life for so long and come to her rescue?
Pretty much the same thing that happened to Sisko at the end of WYLB, happened to Kira. She may be absent from "reality" for a while, but I'd count on her still having a role in the saga of DS9. Maybe not in the next book, or the one after that, but she'll be back, in my opinion.