The story developed in Treason and Blind Man's Bluff showed Nechayev was an operative for an alien race that was seeking to infiltrate and control other cultures. Whether she was replaced or was an alien her an entire life is unknown but I imagine she was replaced.
She's killed in Blind Man's Bluff when the truth about who/what she is becomes known.
It was sort of a cliffhanger ending, in the sense that we don't know what happened to the real Nacheyev, or if she's out there alive and captive somewhere. Plus there's these new bad guys.
I thought the Nacheyev thing was pretty lame - unless they find her and rescue her in a subsequent book, it puts the whole series in an "alternate continuity" because as others have said she is certainly not dead.
Besides, didn't Kersten Beyer just do the same exact thing (though much better done) with a different admiral in Voyager? It wouldn't surprise me if the entire admiralty wasn't just a bunch of alien infiltrators. Like that old episode of Get Smart (or some other comedy?) where the main character infiltrates an international crime organization only to find that every single member has already been replaced by an undercover agent from a different nation.
I really hope Blind Man's Bluff doesn't end up being the last book in the series. Ending it that way, with a buildup and cliffhanger, sucks. It would be nice if they'd at least let him do one more to tie everything up. The series has gone a bit off the rails in the last several books, so I wouldn't be too sad to see it end, but an ending would be nice at least.
As for outgrowing Trek lit? To each his own. I am nearly 40, a lifelong trek reader, and I still haven't outgrown it.

For what its worth the NF series, while sometimes immensely entertaining, is definitely the most juvenile and sophomoric of the series. (The most "grown up" is definitely Vanguard, which just ended.) The recent books in the main trek line have been fantastic as well.