It is indeed a problem to justify the source of morality as anywhere other than the subjective perception of the brain. However, I think most people would agree

It is indeed a problem to justify the source of morality as anywhere other than the subjective perception of the brain. However, I think most people would agree that a rational action or chain of reasoning is rational regardless of the brain, or to what ends. Similarly, most would agree that humans are susceptible to various non-rational behaviours. I'm not here to argue for an objective morality, or the various arguments put forward for moral realism (since I'm not a moral realist myself). Also, the role of intuition in morality (and knowledge in general) is contested. I think that to commit to a system in which we only formalize our intuitions falls victim to three kinds of objection: those who have a reasonable case that we haven't caputered the intuitions correctly, those who doubt the role of intuition in moral decision making (several popular theories, from Kant's to Bentham's result in non-intuitive results in which their proponents will bite the bullet), and those who argue either that moral facts cannot be truthy, or that they can be truthy (but we always get them wrong), or they can be truthy (but we have no way of knowing which are true and which are false).