First, thanks to the author for such an interesting article. What is at issue, I think, are the different forms that knowledge can take.

Knowledge is information that has been sufficiently validated for an individual to accept it as 'true'. For beliefs, that can happen in a place so subjectively deep that even the believer can't explain it. Knowledge can also be rationalistic, based on a preponderance of evidence (as in the social sciences) or based on observation within material existence (as in the physical sciences). A belief that contradicts rationalistic knowledge can be irrational without being immoral--'flat Earthers' being one example.

All moralities, on the other hand, are based on beliefs. To reject a morality (or a position based on a morality) can never be irrational: it can only be (from the perspective of those who accept that morality) 'immoral'. To punish people for having different beliefs is itself, however, a morally charged action.

Finally, there is an ethic ('mutual respect in effecting choices') in the form of 'observational rationalistic knowledge': it follows from the observation that human beings have no choice, in living our lives in this world, but to effect choices (choose among perceived alternatives and take action to bring that choice to fruition). Even then, rejecting the validity of that observation (therefore that ethic) based on belief, though irrational, would not call for 'punishment'; indeed, in asserting that claim a being would be demonstrating one's humanness, ensuring that person all the protections that ethic would afford any person.