Donations received from members and well-wishers should not be taxed. But when a church engages in business (e.g., JIAM's matatus, the Catholic's Insurance company, ACK's and PCEA's rental flats, offices and meeting rooms etc), then the income from that business must be taxed.
Assuming that religious organisations are ran by forthright people, then I do not expect there to be any problem with compliance. All that KRA has to do is write to them and they should do the right thing.
But I guess my assumption is probably too much to expect!