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Interesting, rich conversation.  Like smaley, it made me think of several of our earlier conversations about situations where "scientific" findings come into apparent conflict with other perspectives (cf The spirit catches you and you fall down: a Hmong child, her American doctors, and the collision of two cultures). 
I say "apparent" conflict because I'd like to think that situations like this could be better handled if everyone involved better understood that what is at issue is not "science" versus other ways of making sense of the world but rather differences in the observations being summarized by different people or groups of people.  Yes, there is a body of "scientific" literature consisting of epidemiological studies that indicate no correlation between vaccination and autism.  And there is a body of "scientific" literature documenting the importance of broad coverage for vaccination programs to be effective.  And these ought to be regarded as relevant by anyone making vaccination decisions.  At the same time, these do not, as we discussed in class, compel a particular choice in individual cases.  Epidemiological studies cannot "disprove" the possibility of adverse effects of vaccination in individual cases, and other personal observations are also relevant in the decision-making process of individuals. 
What all of this suggests to me is that the "scientific" community needs to be clearer about the nature of the understandings it offers, the basis for those understandings, and their limitations.  And others need to have a better appreciation of the potential relevance of that for their own lives. My guess (hope?) is that people would be less inclined to dismiss the "scientific" literature if they were more familiar with it and if it was presented as a potentially useful body of observations rather than something "authoritative."  Conversely, I think science would be well-served in its own advancement  by paying more attention to individual variation (as it is in fact doing in some areas).
To put it differently, it seems to me that the vaccine/autism controversy is better seen less as a conflict between "science" and .... other ways of thinking, and more as a situation (one of many) that should encourage greater attention to how scientists perceive themselves, to how science is presented, and to science education in general.  The apparently continuing controversy over the Wakefield paper and its handling is a further argument in this direction, one that might be worth more attention than we gave it in class.  Both scientists and non-scientists are, it seems to me, inclined to attribute to publications in the "scientific" literature a much greater degree of authoritativeness than is warranted.  Maybe the key here is to stop arguing about authoritativeness and what bestows it and get back to making the best decisions one can in individual cases using all relevant observations to date and accepting that decisions always have to be made in the face of some uncertainty. The importance of the "herd effect" in vaccination programs notwithstanding, we can certainly tolerate, and might even be better off accepting, some individual variation in the decisions people end up making in their own lives.