What's interesting is that for TNG, DS9 and (I believe) VOYAGER, they're going to have to update all the standard-def VFX for HD as well, and I think those enhancements will be even more ripe for controversy given how comparatively recent those original effects are, even if they're perhaps not as beloved as TOS.
For me,-- and this applies to STAR WARS and any other VFX upgrade project as well -- I'm not opposed to updating the effects, especially if it's for a newer higher definition format. It's the creative alterations that a new team applies to the work of the original craftsmen who were involved in the project's inception that are to be scrutinized if you care about these things. (I do.) I don't find too many of the TOS Enhanced shots to be worth getting riled up about but I bet there are serious TREK fans who've deconstructed the hell out of them and I wonder what the verdict was or is.