We had a new church get a loan to purchase their building. They currently work under their secretary's TIN. Should the church not have their own number, and is this a violation of BSA since the intity does not have their own TIN and we gave them a loan?

Sounds like it to me. They should have their on Tax ID#.

Yes, the church should apply for and receive its own distinct TIN. There is no reason why they should not have done so already.

My guess is that the issue of real estate property taxes on the property the church purchased may force some action. If the church operates under its secretary's TIN, it will be more difficult to claim exemption from property taxes. And if the church is required to pay property taxes, the secretary will have some explaining to do when the taxes paid are reported under his or her TIN.