Indeed, it may turn out to be the case that we can dissolve the debate between deontological intuitions and utilitarian intuitions if we can map the cognitive algorithms that produce them.

Suppose it's an empirical fact that when people engage in consequentialist-type cognition, they typically use a model of the world that is ontologically crazy (for example, one with irreducible mental entities). Would that be an argument against consequentialism in general? In one sense it is, since it means that we can't straightforwardly translate naive consequentialism into a correct moral philosophy, so the consequentialist approach to moral philosophy is at least more difficult than it might first appear. But surely this empirical fact would not "dissolve" the debate with the conclusion that no form of consequentialism can be right, and therefore the whole approach should be abandoned.

Similarly, I suggest that empirical facts about how people typically form deontological moral judgements can't dissolve the debate between consequentialism vs deontology. A deontologist could still claim, for example, that while the typical deontological rules people naively come up with to explain their intuitive emotional judgements are not very good, intuitive emotional judgements are still the only source of "morality" that we have, and some set of more sophisticated deontological rules fits those intuitions better than any other moral philosophy, including any form of consequentialism.

ETA: Perhaps it would make more sense is to say that the specific deontological intuitions that people tend to naively hold (such as "lying is always wrong") can be dissolved with more scientific self-knowledge. On the other hand, it seems plausible that many of our consequentalist-type "values" can also be dissolved the same way. (See my previous comment.)