Note that philosophers usually have the same judgments as 'common folk' on trolley problems (Fischer & Ravizza, 1992).

'Course, but mere correlation of binary judgments tells us little about the similarity of causal mechanisms that lead to their judgments. We should expect philosophers to have more reasons, and more disjunctive ones. Even overlap of reasons doesn't necessarily give us license to imply that if deontologist philosophers weren't biased in the same way as common folk are then they wouldn't be deontologists; we must be careful with our connotations. True beliefs have many disjunctive supporting reasons, and it would be unwise to presuppose that parsimony is on the side of deontology being 'true' or 'false' such that finding a single reason for or against it substantially changes the balance. If you want to believe true things then your wanting to believe something becomes correlated with its truth... "rationalization" is complex and in some ways an essential part of rationality.

All that said, Schwitzgebel's experiment does seem to indicate commonplace 'bad' rationalization. (ETA: I need to look closer at effect sizes, prestige of philosophers, etc, to get a better sense of this though.)

Did you see the bit where Greene explains in more detail what he means by these terms?

Yeah, and I see their logic and appeal; still, the equivocations seem to be unnecessary and distracting. (It would've been much less contentious to use less provocative terms to describe the research and then separately follow that up with research like Schwitzgebel's; this would allow readers to have more precise models while also minimizing distraction.) If this were anywhere except Less Wrong I'd think it was meh, but here we should perhaps make sure to correct errors of conceptualization like that. This has worked in the past. That said, it would have been more work for you, which is non-trivial. Furthermore I am known to be much more paranoid than most about these kinds of things. I'd argue that that's a good thing, but, meh.

Were there, for example, methodological problems with the studies linking deontological-style judgments to emotional processing, or with the studies linking utilitarian judgments to more 'cognitive' kinds of mental processing?

Neither, the "relevant parts" I was speaking of were the parts where he argued that Kant and other philosophers were falling to the same errors as the members of the studies. I still find his arguments to be weak; e.g. the section Missing the Deontological Point struck me as anti-persuasive. However Schwitzgebel's experiment makes up for Greene's lack of argument. Are there any meta-studies of that nature? (Presumably not, especially as that experiment seems to have been done in the last year.)