I'm of absolutely real help to you, since I've not touched Morrowind since it was new and shiny, and if memory serves didn't mess with modding beyond a home for my character. What Morrowind data do you hope to preserve, should you decide to reinstall? If it's only save-files, won't a new install recognize and load those saves, assuming they don't contain coding from a now-gone mod that simply must be present for compatibility? I know I can transfer saves without issue when I update DFU. Then again, my DFU is mods are almost wholly graphics improvements, which don't (or shouldn't) affect gameplay.
If that is indeed the case, find where those saves are kept, then make backups of them, stored in a "safe" area on your PC. If uninstalling the game deletes those saves, which it might not, you can restore your backups to their original location. But again, this is just me guessing.
--------------------
|