That seems strange, since it does appear on my Add/Remove Programs list, and DGIndex hasn't been acting wonky either (especially considering that the version I index with is 1.4.6, and the version of DGDecode is 1.4.8, which I assume is what MeGUI had installed - I didn't even know they were mismatched

).
Have you updated through MeGUI to the latest versions? Or is that what caused the problem? In either case, it should be possible to simply get the right version of DGDecode.dll from
the official site and replace the one that's in AviSynth's plugins folder with the version that matches the version of DGIndex you used before. Just go into the version of DGIndex you used to make the d2vs that don't work now, and then to Help->About DGIndex, and it'll have a version number. Just download that version number's package from the site, unzip it, and swap the DGDecode.dll in AviSynth's plugins folder with the one from that package.
If you can update MeGUI, it might give you the uninstaller program. The update function should either pop up on its own, or it can be found in Tools->Update. If it's not there, I would be under the impression that it's an old version of MeGUI that didn't have the capacity to update, but I didn't think those versions came packaged with AviSynth plugins and whatnot.
Otherwise, I guess you could just delete MeGUI's directory. I wouldn't assume it has anything system-vital in it (didn't seem to before, at any rate - then again, I just unpacked it out of a zip file in those instances, not through an installer), and if you run something like CCleaner and/or go into regedit, hunt down all references to MeGUI and delete those too, it should be alright.