Dale, interesting information, isn't it? I had never heard of it before, but just ran across it while researching something else. I copied some additional correspondence on the subject, which I'll post sometime today.
The instructions regarding the seizure of M. E. South churches were issued pursuant to an army-wide circular letter sent to all department commanders, but the Department of the Missouri is the only command I've read about thusfar which issued orders on the matter.
The Bill of Rights sure took a beating during the war, didn't it?