I realized this as soon as I submitted it, but was pretty sure I had no recourse, but then I decided "what the heck, I'll ask GradCafe".
First, just to be clear, I have the absolute highest admiration for the theory that goes on at Berkeley. All of it. Including related stuff in non-CS departments. They are one of the world-epicenters of CS theory, with paradigm-forging researchers, no dispute. I would love to go there. At the same time, it's probably a reach for all those reasons above, and I have some other acceptances already, so I feel less bad about my mistake, but still bad. I would love to have the option of Berkeley, but well...
Stanford is great too, but my Berkeley app doesn't win any points in the Stanford admissions process, so...
So, I'm aware this is kind of a big mistake, and I don't have any way to fix it at this point. Was I right to just wait it out and hope they laugh it off? (I do correctly name them, including specific professors, in some passages of my SoP!) or should I have sent/send a letter of contrition, begging them to overlook it?