The disc brakes are good at all speeds and by mounting it to the jack shaft, it's effectiveness is also enhanced by the gearing, meaning it'll take less squeeze on the brakes than if mounted to the rear wheel (you may only need one finger for the rear brake with this setup to prevent locking up the rear wheel), however, mounted to the jack shaft, that also gives the engine more leverage to resist the brake if the throttle got stuck open compared to wheel mounted, again, because of the gearing, the engine may be able to overpower the rear brake in a throttle stick situation so be sure to double check your throttle system for no binding and that the return spring is affixed well with no way to pop off etc. Having the kill switch in easy reach is another good backup in case of a throttle stick too.
I'm guessing you're running a cable actuated caliper right now, which should be ok, but if you need even better rear brake effectiveness and control, you could switch to hydraulic, which entails getting a new system, the lever/master cylinder, the line, and caliper. What's nice about the hydraulic brake setup is that you can run more than one disc and caliper if you do need more stopping power.
I would focus most my braking effort to the front wheel also because you can only use so much rear brake before the rear wheel locks up, usually, the front brake does about 70% of the work and the rear helps out with the other 30% because the tendency to lock up is much greater with the rear brake than the front.