I think the writer's point could be valid and I think it comes from honest concern about shows that he likes, I just don't think it really applies to Sherlock. If the references would be impossible to understand if you didn't follow the discussion, then he'd have a point, but everything fits into the narrative. And there weren't so many references anyway, just the two fake theories, one is a killer hook, the other a funny intermezzo, both of them would work perfectly fine for people who had only seen Reichenbach and wanted to know the conclusion.
I think the main reasons why people might not have liked the episode is unrelated to fan references. The episode is the denouement of series 2 and the introduction of series 3, told in Mark's signature 9 acts. However, people expect a film; a self-contained narrative with a strong central conflict told in three acts. If that's what you expect, then you might get disappointed and blame it on the fans. I honestly believe that had the same story been told in three, with more attention to the baddie, than no one was complaining right now. It's just a difference in expectations, and the difference between a film and a series.