There's now a theoretical paper up on the arxiv discussing a lot of these issues . The authors are respected physics people it seems. I have neither the time nor the expertise to evaluate it, but they seem to be claiming a resolution between the OPERA data and the SN 1987A data.
http://www.nature.com/news/2011/110922/full/news.2011.554.html
http://arxiv.org/abs/1109.4897v1
http://usersguidetotheuniverse.com/?p=2169
http://news.ycombinator.com/item?id=3027056
Perhaps the end of the era of the light cone and beginning of the era of the neutrino cone? I'd be curious to see your probability estimates for whether this theory pans out. Or other crackpot hypotheses to explain the results.