Yes, and for many churches it is the most cost-effective approach. Heating the full volume of a large nave when only a few rows of pews are occupied wastes energy and money.
Radiant systems, particularly infrared heaters, are well suited to zoning because they warm surfaces and people rather than air. You can direct heat at the seating area and leave the rest of the building unheated without physical barriers. Switching zones on and off is as simple as flipping a circuit.
Wet radiator and warm-air systems can also be zoned using thermostatic radiator valves or ductwork dampers, but the effect is less precise because heated air moves freely through the building. Underfloor heating zones are set at installation and cannot easily be changed afterwards.
If your church hosts different activities in different spaces, a clergy vestry used daily, a nave used weekly, a hall used for community events, zoning lets you match the heating to the use rather than heating everything all the time.