3E was marketed as a "return to the dungeon". They wanted to be linked to 1e, not 2e, and that meant, among other things, having Gary saying "I'm Gay Gygax and I endorse this D&D". And that's, more or less, what they paid him for, and what he did in his Dungeon/Dragon (I don't remember which of them) articles.
But there's a difference between what one's paid to write and what one wants to write. Gary was very polite and respctfully avoided the aspects he didn't like abut 3E when he wrote for WotC, but when, around the interwebs, he was asked for his opinions by fans, he answered with the truth. And the truth was that he didn't like many of the new D&D's trappings. And he did it vehemently, for he was a vehement person.
A man is entitled to his opinions, and Gary had his, and expressed them when asked. It was not out of charity that WotC had him writing those articles, but an act of marketing. Gary could be a man of strong opinions, somewhat grumpy at many times, and perhaps a little too paid of himself and concerned about monetary issues, but he was definitely nor a liar nor a hypocrite.