Mr. Burlew claimed that he was going to bring it over so that it was some vague gray area between 3.5E and 4E, but that certainly hasn't happened. Also, it is not like he has stopped making any jokes based on rules...
Seriously, in a very recent strip he turned the fairly obscure and very minor "can't sneak attack a rogue unless you are 4 levels higher" rule from 3.5E into a plot point within his strip. It was involved in a critical mistake on a character's part that lead directly to a fairly major event. Actually, that same comic had a punch-line/final quip that doesn't even make sense under 4E assumptions. No matter how much the strip is more focused on its own story than on rules jokes, it doesn't change the fact that D&D rules are a very important part of that story.
Also, Mr. Burlew continues to base all of the races, classes, and monsters in his strip on 3.5E races, classes, and monsters. He hasn't even made a single move to introduce a Warlord, or a Dragonborn, or one of the new 4E Angels, or anything.
I don't think a complete conversion is necessary at all, but right now Mr. Burlew seems to be doing nothing more than pretending that 4E doesn't even exist. He has certainly not held to his claim that he will make some kind of transition. If he just said outright that he was not going to make such a transition (like some other D&D based comic authors have made), then I would have no problem (other than a disagreement, I suppose, but one I could just ignore and keep to myself), but he did not go that route.