That would only get rid of half of the problem. You are forgetting all those excessively DNRed live action sequences before FX scenes. They themselves are at least as jarring as the poor effects work from HTV.
I haven't forgotten the excessively DNRed live action scenes, there just isn't much that can be done to save them...well, nothing beyond adding a layer of grain...and perhaps splicing in new images on the screens if possible.
As for CGI, I prefer that CBS use the original elements as they have chosen to do, but in the case of Season 2...fan made CGI may be the only solution. So if it can faithfully reproduce the original shots at CBS-D quality, I would accept that over what HTV slapped together.