there's one way I can imagine the DS9 Typhon Pact novel to work well and not obliterate the current storylines - do something astoundingly out of the blue, like only one or 2 faces that we know, and then spend the novel fleshing out the TP side of things without advancing a DS9-specific storyline. To some degree, this will be happening anyways - we know Ezri and Bowers aren't going to be around (they're off on Aventine), we'll find out soon where people end up after Soul Key comes out, etc. It's not impossible to imagine, in a story having taken place 5 years after the last time we see everyone, that there has been significant turnover. I mean, while I'd miss some characters, I can imagine a DS9 story in the post-Destiny track where the only character we know up front is Quark (and throw in a transfer we've seen in other places). That doesn't mean characters like Kira and Bashir are gone forever, but they could have moved on/had something happened, etc in that 5 year span.
I guess what I'm saying is that a jump like that provides lots of possibilities, and the DS9R has been so quality so far that I've got faith it'll be handled in a way that works within the stories we've seen, doesn't significantly shortchange the characters, and doesn't make it look like the DS9 universe was static for 5 years.