Personally, I never do, as I install it into a copy of the original Civ3 folder. If you plan to play GOTM in future than I would recommend that you do the same, as you can then alternate GOTTM and normal games.
However, uninstalling is not a big deal. There are only two, possibly three incompatible files as far as I am aware:
1. There's a pair of files called resources.pcx and resources_shadows.pcx in the /Art folder. You need to swap these out for the original pair, which should be stored in "/Art/resources storage/my original resources folder".
2. The pediaIcons.txt file may not be backwards compatible, although I think Bluebox's mod includes a file that is supposed to be. If you want to revert to the standard one to be safe, you should find it stashed away in the "Before GOTM23" folder.