I really don't think it's a shame. He wanted to faithfully recreate the scenes in CGI. I would actually love to see a fan project that faithfully recreated season 2 with CGI, and do it well enough that we could splice them into the bluray season 2 episodes and forget HTV ever happened.
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.
Also, I agree with what others have said that CGI could not really live up to the model work when it is assembled properly with correct lighting, grain etc.