Why can't you pedal in all your gears with a hub motor? I think you're confusing overheating the motor with too much throttle and not enough RPMs/speed (on a hill for example), which could/would actually be solved by making use of all your gears.

Also hub motors come in geared and gearless versions. You'd probably be less likely to encounter overheating problems with a geared version. Geared versions allow the motor to operate at higher RPMs where their are more efficient.