Given your sort of use then it is to be expected that the rear brake discs would suffer severe rusting and pitting. Brake discs rust all the time. More so in winter due to salt on the road and trapped condensation inside a non-heated and non-ventilated garage. The more you drive the more the effect of braking removes surface corrosion from discs. But in normal driving the front brakes do all the work. The pads don’t touch the rear discs much unless you brake really hard from high speed. So what has happened is normal. Nevertheless, in this situation, Honda dealers have been replacing rear discs on Civics under the 3 year 90,000 mile warranty.