As far as I remember, Porygon had nothing to do with those seizure-causing lights. Pikachu just blasted away some... vaccine... missiles, or something (and I though the needles were scary!!).
Porygon was just the only main Pokémon in the episode not belonging to one of the main characters of the show, and therefore people would associate Porygon with the episode. I guess.
I'd like it if they brought back Porygon (and showed its evolutions). I think it's time to move on from the incident-not-caused-by-Porygon-but-which-Porygon-was-blamed-for. Stop living in the past, guys. ; ^ ;
...Besides, Porygon was shown in an episode airing after the banned one. The one with the hospital, I believe. It also appeared during the opening of many movies (all the way up to the sixth one, I believe), so... :I