Heck, I've seen people object to "Assignment: Earth," and even insist that it's not a real Trek episode, because it's actually a backdoor pilot for another series. Was Trek "contaminated" by Gary Seven and Robert Lincoln?
Look, there are characters and episodes in every Trek series that I'm not particularly fond of, but I'm not going to take offense if a novel references "The Alternative Factor" or "Friday's Child" or whatever. "How dare you remind me of that sucky episode!"
Like it or not, it's all Trek. The new movies included.
So, yeah, Romulus is toast.