Churches are not exempt for the purposes of the Feed-in Tariff even though they are normally exempt from EPC's the rules are :
"2.90. A relevant building must also be a building in respect of which an EPC can be issued. If an EPC cannot be issued then the building is not a relevant building and the energy efficiency requirement does not apply. Under the EPB Regulations some properties are exempt from the requirement for an EPC; however if a building can be assessed and receive an EPC then the energy efficiency requirement will apply under the FIT legislation (irrespective of whether an EPB exemption applies or not)."
So although for a normal EPC a church is considered to be 'not a relevant building' the point of this particular clause is that it is possible to assess it.
So, in effect you MUST have an EPC of D or greater for the church , or else accept the lower tariff.
Some modern places of worship of course can meet this criteria.