When I first read it, I was pretty upset. I went for a walk, grabbed lunch (trying not to cry), and then went back to read it again. I started writing my response - what I really wanted to say (making sure not to have any email addresses in the "To:" field, just in case!). That was very cathartic, and I was then able to edit it so that it was respectful, yet still got the point across. I even brought attention to his accusation, by using the absolutely wonderful technique of "I'm sure you didn't mean to attack my character and insinuate that I *enter bad thing here*, as that was not my intention." To score yet another good-confrontation point, I added at the end how we could work together to solve the issue.
I felt really good about myself when I sent the email back, and wasn't really worried what his response would be (which is a huge step for me). I knew that I handled the situation with grace and respect. He emailed back, saying he thinks it would be a great idea for us to work together, clarified some of the things he was talking about before, and even apologized for what he said! After another couple emails back and forth, things seem to be settled.
I am so proud of myself! Now, if I could only translate email confrontation skills to in-person, I'll be set!