Yes the heater valve should be freed up first. I remove the heater hose going into the firewall to the water valve. You can then spray the penetrant directly into the valve itself. Warming the valve with a heat gun also helps before attempting to move it. If your plastic heater flap is broken, remove the little intake air hood, in front of the windshield, you then can remove the flap and repair or replace it. If the heater water valve is badly stuck, you will have to remove the inner cylinder and clean the bore and the cylinder itself (steel wool works good). Do not drop any parts when working on the water valve, also do not push too far downward on the cylinder. It can fall through into the heater core.
Let us know if you need to remove the cylinder in the heater water valve. Additional information will follow if needed.