Depending on how far you are and how much you care about what you've got, restarting with only the FMP (which does include some of the Terrain Pack, so it's not like you'll be playing only with vanilla terrain) is certainly the easiest solution. If you restart, I would recommend Solarius' other mod: XComFiles, which has been a blast even though it's not quite finished. It's a kind of FMP++, if such a thing is even possible. And it has a whole bunch of terrains.
If you don't want to restart, I would suggest you start a game with FMP only (No terrain pack!), create your base and save immediately. The idea is to generate a clean FMP mission table, which is a list of all possible alien missions. Since you have only the FMP enabled, you'll have only proper FMP missions. In that save, find the section called "alienStrategy" and copy the whole thing. Take the save you want to keep, go to the "alienStrategy" section and delete everything, then paste in what you got from the clean start.
This will re-enable some missions that you've already gotten, but that's not much of an issue. The most important thing is that it will remove from the list of possible missions anything that was created by the Terrain Pack and allow you to remove all influence of the Terrain Pack on your game. (Make sure you also turn off the mod in options, of course). Only turning off the mod without the save fix wouldn't remove the entries from "alienStrategy" in your save. It would just not load the assets and that would be even worse because then any Terrain Pack specific mission still in your save would crash the game.
Mixing mods is a tricky thing, especially when you play around with big ones.
