I thought the comic was pretty different in portrayal as well. I think Ian garnished the stupid a tinsy bit thick on Knuckles to be honest. Strange, because like you said, Knux wasn't particularly stupid so far in the show (granted he was mostly in the background, but still).
My theory for the difference? This comic was likely written when the show was in production and Ian was only given a rough idea to work with. It's either that, or this is just one of his weaker ventures as far as I can tell. For now, I'll just wait and see whether TV Knuckles is the right portrayal, or comic Knuckles is. It's too soon to call how he'll turn out.