Is there a way to disable upgraded special agents?

Unfortunately, no. Once you unlock the Pro Agents, they will remain the Pro variant for as long as you don't reset your progress.

The purpose of the Pro Agents is to provide a more useful alternative to each agent as a sort of reward for purchasing 50 of the same agent collectively. I guess if the Pro Farmer is causing you problems the only option is to keep the farmer out of reach from the track or close to the exit if possible.