I'm curious. What was it that she said to make him think she was "cheating"?
This also makes me wonder what it is she's said to lead him to believe you're clueless to the whole thing. If she has said you're sitting there at times and he doesn't believe her, my thought is that it's from something she's said in the past.
As you've said, he's the innocent one here and should not be blamed for his thoughts and feelings. But if thoughts and feelings are to come into play (and they should), then honesty MUST play a factor. Have you been seen on cam during regular chats? When she says you're there and in fact you are, do you show your face and let him know you're part of things at that moment?
I know it may be difficult because what seems to be a good online friendship for your wife may be lost, but total honesty is the way to go (in my opinion). If she lets him know the situation, that you've known all along and this is a fantasy, he may be receptive to it. He's already aware that she's had thoughts of threesomes. He said he's not into it, and I'll assume he's aware this will only ever be an online thing. With that in mind it may be easy for him to play into your fantasy as he has unknowingly all along. Who knows! Being the "backdoor man" may be a turn on for him and things can continue with everyone's fantasies being satisfied!
Good luck and great sex!