A recent study by folks at the Oxford Centre for Neuroethics suggests that Greene et. al.'s results are better explained by appeal to differences in how intuitive/counterintuitive a moral judgment is, rather than differences in how utilitarian/deontological it is. I had a look at the study, and it seems reasonably legit, but I don't have any expertise in neuroscience. As I understand it, their findings suggest that the "more cognitive" part of the brain gets recruited more when making a counterintuitive moral judgment, whether utilitarian or deontological.

Also, it is worth noting that attempts to replicate the differences in response times have failed (this was the result with the Oxford Center for Neuroethics study as well).

Here is an abstract:

Neuroimaging studies on moral decision-making have thus far largely focused on differences between moral judgments with opposing utilitarian (well-being maximizing) and deontological (duty-based) content. However, these studies have investigated moral dilemmas involving extreme situations, and did not control for two distinct dimensions of moral judgment: whether or not it is intuitive (immediately compelling to most people) and whether it is utilitarian or deontological in content. By contrasting dilemmas where utilitarian judgments are counterintuitive with dilemmas in which they are intuitive, we were able to use functional magnetic resonance imaging to identify the neural correlates of intuitive and counterintuitive judgments across a range of moral situations. Irrespective of content (utilitarian/deontological), counterintuitive moral judgments were associated with greater difficulty and with activation in the rostral anterior cingulate cortex, suggesting that such judgments may involve emotional conflict; intuitive judgments were linked to activation in the visual and premotor cortex. In addition, we obtained evidence that neural differences in moral judgment in such dilemmas are largely due to whether they are intuitive and not, as previously assumed, to differences between utilitarian and deontological judgments. Our findings therefore do not support theories that have generally associated utilitarian and deontological judgments with distinct neural systems.

An important quote from the study:

To further investigate whether neural differences were due to intuitiveness rather than content of the judgment [utilitarian vs. deontological], we performed the additional analyses....When we controlled for content, these analyses showed considerable overlap for intuitiveness. In contrast, when we controlled for intuitiveness, only little--if any--overlap was found for content. Our results thus speak against the influential interpretation of previous neuroimaging studies as supporting a general association between deontological judgment and automatic processing, and between utilitarian judgment and controlled processing.” (p. 7 my version)

Where to find the study (subscription only):

Kahane, G., K. Wiech, N. Shackel, M. Farias, J. Savulescu and I. Tracey, ‘The Neural Basis of Intuitive and Counterintuitive Moral Judgement’, forthcoming in Social, Cognitive and Affective Neuroscience.

Link on Guy Kahane's website: http://www.philosophy.ox.ac.uk/members/research_staff/guy_kahane