Having ones work superceded by events is something novelists and other writers simply have to deal with and not just in the Treklit field. In my personal opinion (and that of others I've seen commenting here) one of the best Trek novels ever was "Federation", which was totally contradicted by the film "First Contact", one of the best films ever. Am I supposed to not enjoy one or the other because of those contradictions? Not at all.
Quite right. Quality and continuity are two completely separate considerations. Since all Star Trek
is fictional anyway, being out of continuity doesn't make a story less "true" -- none of it is true. It's just a bunch of elaborate lies for our entertainment. Some of those fictions are consistent with each other, some are not, but it's all just pretend, so what's the harm if some of the pretending goes in a different direction from the rest?