I looked into the developer's site and it can apparently be circumnavigated by merely unchecking the emulation tools themselves in the programs options. This is a slight hassle, but not nearly as bad as completely uninstalling. That's only the official fix anyway, I would assume there are less legit, yet better, ones.
Personally, this kind of thing really pisses me off. This is like if I tried to watch a movie and a screen came up saying "Oops, it looks like there's a RECORD button on your VCR... I guess you can't watch this." I have half a mind
to actually pirate these games and then return the retail copies, just because of this crap