Yeah, probably would be difficult. You'd either have to set a minimum score (say 5 points) before they'd qualify as a medic class for auto-balancing (to avoid exploiters), or set limits on the class. Each team is allowed 1 medic. If both teams have one medic, then each team is allowed the option of a second medic, etc. Keep it a dynamic limit that forces the other team to never have more than a one medic advantage. If a medic drops or changes class, the other team is forced to adjust when one of their medics dies.
I know that's against the spirit of the game, but the game would be pretty much perfect with no medics. (Sure it's better when both teams have 2 or 3 medics), but with no medics you'd have great balance. No matter how a team stacked a class, you could easily counter it. The only counter for medics, is for your team to have medics. And since most people find it boring to play, teams often go medicless. Even when the other team has 3 on defense and you're getting your ass kicked on offense with 0.
I know that's against the spirit of the game, but the game would be pretty much perfect with no medics. (Sure it's better when both teams have 2 or 3 medics), but with no medics you'd have great balance. No matter how a team stacked a class, you could easily counter it. The only counter for medics, is for your team to have medics. And since most people find it boring to play, teams often go medicless. Even when the other team has 3 on defense and you're getting your ass kicked on offense with 0.