There are, unfortunately, no easy solutions to this problem. At least, for non-modders, anyway.
There are ways of making the mod faster. I've implemented most of them in my mod Final Frontier Plus, but that's not for Star Trek, it's for Final Frontier. And while deanej wants to merge that with Star Trek, those methods require you to compile a new DLL, and I'm guessing you don't want to do that.
There are a few things that could be done more easily in Python only, without any recompilation, but they probably don't amount to much.
I can give you technical details about why the mod is slow, but that's probably not what you're looking for.