I am opposed to muzzling clergy. Is there a distinction to be made between a small church where the charismatic pastor is the only spokesperson and a church-corporation like the Vatican Church? The charismatic pastor should not have to leave her First Amendment right to free speech at her church door and when she ascends into her pulpit, she should be allowed to say whatever she wants (short of libel, etc.) Figure out some tax solution other than taking away human rights. Whether church-corporations are 'persons' entitled to free speech is another issue.
 
Certainly the Constitution does not end at the church door and misogynist/homophobic church organizations should not be exempt from laws that make it a crime to discriminate in employment. For sure, only certain types of activities are church-related. Building a wealthy all-male hierarchy cannot be construed to be a legitimate church activity any more than performing a marriage to a child-bride can be a legitimate church activity.