Which Star Trek mod? At my last count, there are two released Trek mods for Rebellion, ours, and STA3.
If you're having trouble with downloading, the mod download may have corrupted, but it's probably just Moddb, there have been complaints about people getting corrupted downloads for a long time there.
Playing normal Sins instead of a mod is a simple issue of deactivating the mod. There is an EnabledMods.txt file in the mods folder that sets which mod loads, if any. They do not overwrite the install folder, your original game remains untouched.
As far as authoritative sources of information go, there is some info up on our SOA2 page in the form of general faction tips, and since I designed just about everything, I also know and can tell you everything, even things you should really find out for yourself. I'm not sure if there are any places for STA3 info, that team was really big on advertising, which gave them a pretty big following, but I don't remember any wiki's or faction overviews.