this is more like your boss ordering lunch for a team, and sending a form with options for meat, vegetarian or other. but rather than selecting vegetarian, you select other and put in a screed about how eating animals is wrong.
If he had refused to put pronouns entirely he probably would have been fired anyway. By doing it this way he at least has a shot of a religious discrimination suit.
I don't think he does, because his religious beliefs are accommodated: as a Catholic who believes God created him as male, he can select "he/him." The pronouns he uses were listed there for him to pick. The form didn't ask him to elaborate; he chose to. He was protesting the existence of the question because it gave other people an option he personally chose not to exercise - protesting that option is like protesting having pork as one of several options for team lunch, vs. just choosing not to have the pork.