They aren't stopping with the effects shots. The analog chronometer on the bridge's navigation console was replaced with a digital one in tonight's episode. If the originals are made available on whatever HD format wins out, I can live with these pointless alternate versions. But if they don't, saying "they're on DVD" will be as weak an argument in a decade or two as Lucas' old argument that fans who prefer the OT have the VHS tapes to watch.
Interestingly enough, the CGI for the new cut of the first Trek movie was not done in HD. That will come back to bite Paramount in a couple years!