Damned if you do, damned if you don't; people here are going to accuse him anyway, because it fits the David vs. Goliath narrative.
You don't seriously believe that do you? If he did that there wouldn't even be a thread here.
"Former Reddit worker does an AMA; CEO talks to him privately about why he was let go" is not nearly as catchy.
Don't forget that just before Reddit's CEO commented, this guy was a hero of the thread; his comments could have started a completely different discussion.
If you need to deny it, you can say, "This isn't an accurate account of events" and leave it at that. But even that's unnecessary.
Sure, this guy was phenomenally stupid to start a pissing contest with his own employer on a forum said employer controls but that whole pig/mud thing is really true.