The right to protest and peacefully assemble doesnt give you the right to do it in private property. The church is church property its open to its members and generally the public but that doesnt make it a public place or public property. If you want to protest a store, you are free to do so on public property outside the store. You are not free to do so inside the store disrupting the purpose of the establishment. The store is private property they are within their rights to refuse your business as long as it isnt based on a protected class.

A church really isnt any different, their business is worship and offering a peaceful place for contemplation, reflaction and prayer. If you disrupt that they can and should ask you to leave and should you refuse that becomes the crime of tresspass.

If you want to be empowered by your rights then you should first take the necessary time to understand them.