Good to hear that some people have been successful, which at least means that this is once again just localized bad luck with people not knowing about EU law.
I'll print out some materials on the UKBA website that illustrate that the EEA rights are based on our marriage and not on what her passport says, but might have to get the PCT involved. My biggest fear, however, is that they also know sod-all about the interaction between NHS law and EU law, and that they'll basically turn me around. This is rather specific paranoia; the last time I called them, asking a question about my medical card, they asked me if I had an EHIC.
I replied, "of course I do... Courtesy of the NHS, because I LIVE HERE and after 3 years am probably not a 'visitor' from another EEA member state." I did win that argument, though I'll admit that it was a bit of an unfair one because I'm getting a PhD in European Law and teach this stuff to 19 year olds 2 times a year.
Edit: thanks for those links, but I don't think that the first one actually represents a correct interpretation of the law, and the EU Signpost service has my back on this. Basically, what that guidance is trying to argue is that it would be unfair if EEA students were entitled to the NHS. That may be, but if the UK has a problem with that, it needs to change its 'access to NHS' laws. Otherwise, the law says that 'students' have this right without qualifications other than length of course; to suddenly start denying the right to European students would be discrimination on the basis of nationality. Universities, in any event, basically don't seem to agree on this point either: EEA and course shorter than 6 months, entitled on the basis of EHIC; EEA and course longer than 6 months, entitled period + family. So I should be fine!