Yes, I think he is. I think somewhere the truth is that Tommy, Joe and Misty were in that mobile home early in the evening and a party ensued. What happened after that is anybody's guess. I STILL think Ron, Jr. was the best and only honest witness. One of the two males took Haleigh out of her bed. I shudder to think about the bouncing couch. Then, perhaps, she was murdered because she was so badly injured they all feared both her father and his rage and what would happen to them all in the legal system.
About Joe's "I didn't do it." He must know there is an "it" that was done. that alone sugests to me that he knows what happened. Otherwise, he would have said, "I am not involved in Haleigh's disappearance." The "it" has to be something, in his mind. For example, a kid sees an angry parent and says, "I didn't do it" even before the parent asks, "Who broke the lamp?" That's a kid with guilty knowledge, either guilty of the act or knowing what happened and who did it.