Sorry, none of your examples hold up as appropriate for this context. St. Athanius wasn’t disobeying his religious superior, Joan of Arc wasn’t a confessed religious, and St. Paul cries out against disobedience.
In this case, with this priest, his comments are inappropriate, whether the comments are correct or incorrect.
His comments are appropriate under the circumstances, and furthermore, he deserves credit for speaking the truth with charity.
What you seem to be advocating for is a form of clericalism which is divorced from truth and justice. God bless Father Wylie, and may He send us many more courageous priests who are able to discern the difference and speak the truth when justice demands it.