A church supports various ministries. If a check is written to a ministry (a tax-exempt organization), does a church issue a Form 1099-MISC to that ministry. The church leaders understand that it is to issue Form 1099’s when it compensates individuals in a ministry.
The posted question concludes: "The only thing we can find is that in general we do not have to issue a Form 1099 to a corporation."
One of the exceptions to required reporting of payments listed in the 2010 instructions for Form 1099-MISC is "payments to tax-exempt organizations." Therefore, payments to a ministry are not reportable.
Churches that pay rent, services, etc. to individuals who are not employees (they receive Form W-2) must file Form 1099-MISC.
Thanks to the Patient Protection and Affordable Care Act of 2010...
Regarding the last sentence in the above Question, beginning with payments in 2012, for-profit corporations that are paid by the church for rent, services, etc. must also receive Form 1099-MISC from it.
The penalties for non-filing and for failure to withhold Backup Withholding, when required, are steep and will increase in 2012.