I've switched all of my flying from SJC to SFO when possible for multiple reasons, one of which is the presence of the ionizing radiation backscatter scanners present at SJC v. the MMW at SFO. I have little problem with the safety of the MMW scanners. Privacy is still a concern, however. (..and it will continue to be until ATD is tried and true and the glass viewing booths are removed.)

I've only had to opt-out once at SJC, and that was June 2010, so my data point is likely obsolete. They didn't gave me any problem back then, but this was right after they had installed the NoS at the A checkpoint and before all of the bad press. It was still the back of the head procedure, and the comment at the time was, "You're opting out? Ok. Just walk through the metal detector and wait for an assist."

Your airline will typically determine your success in avoiding the NoS. Due to the low amount of traffic, there's typically only one lane open in Terminal A, with all arrows pointing to the BKSX. Terminal B allows for better self selection of lanes - or at least it did a few months ago. As a primarily AA person, I narrowly dodged having to opt-out in December during a window where the machine was roped off. (I saw it get roped off while I was getting in line to the TDC, and it was in use again when I walked by 15 minutes later.)