I like BN's suggestion here:
Butterfly North wrote:Something along the lines of 'I don't want to say any more than this but over the course of the weekend your wife has made it clear she believes some pretty strange things about me. I think you should talk to her about it.' That way if she refuses to discuss it with him at least you've given her the opportunity to do so in her own words.
because not saying any more than that at least means that it can't be construed as you saying to your friend "ha ha, your wife thinks we're sleeping together, isn't that crazy?" (if she thinks that you and he had this big conversation all about it and all about her, that's probably going to make her more insecure ...).
Thinking about it, I would try to avoid email (unless you already email with her regularly but I'm guessing that's not the case) because it's so
easy for tone to be misconstrued or words to be misinterpreted. But if that is the only option, I think sticking to things that you're happy to be repeated / don't think can be misinterpreted would be good, like Sonic suggests. "I'm really confused, I don't understand, I don't know where this idea came from" rather than "you must be crazy to think that, how could you say such a thing, of course we've never had sex" (especially as she might discuss an email from you with her friends/mother/etc, and things might sound quite different from their POV as they might not know you).