Here are a couple questions about the hardware you have and what you might be able to do.
Are you using high pressure LP burners (10+ PSI), low pressure LP (13" WC), or Natural gas (4"WC).
What is the temp controller output on/off relay, 0-5 VDC, or 4-20 MA
With furnace valves you are limited to Natural gas or low pressure LP type burners and on/off operation. With high pressure LP there are few options for pilot safety valves and most folks have gone the electric ignition route with solenoid valves for on/off operation. If you are determined to vary the fire rate there are devices called mass flow controllers that will electronically vary the gas flow in response to a 0-5VDC or 4-20MA signal. I have 2 of these devices in operation on the phase 2 brewery but would say that they require high pressure(10+ PSI), multiple output power supplies, and a much more involved design and control scheme than most folks want to do. There are PWM low pressure furnace valves available but price and control methods are more than most want to deal with.