I don't know anything about Roy Dean so I can not comment there, but I don't find MMA barbaric at all, but it is just a sport. I don't see strict MMA training as a viable self-defense method because you are working within a rule system, which doesn't exist in true self-defense situations. I also don't really find boxing all that viable either, although I know many who would disagree. Not to mention you don't train against multiple opponents, like you would at the higher levels of Aikido training.
I see no need to remove Atemi from Aikido, sometimes it is necessary .... but self-defense can be intellectualized, just to a certain point. I think a lot of people miss the point that the moves you learn in Aikido are a starting point for you to develop your own effective "style" (approach may be a better term here). No one person's style (approach) is effective for everyone, and you must do what works for you. For me it includes Atemi, and some groundwork as well.
You and I we will likely disagree that Atemi is "necessory for self-defense" (your quote), because I don't believe to be effective in defending youself you have to strike, but, this is based on my subjective experience, as your opinion is more than likely based on your subjective experience (or vicarious experience / anecdotal evidence which essentially equates to the same thing). Like I said, to me Aikido gives me the option to use "gentler" methods, something that other arts do not provide. But, there are times to use Atemi as well .... whether it should be taught at lower or higher levels of learning is another discussion entirely.