My experience isn't with MC boots getting that worn, but the heels of my hiking boots can wear through if there's too much sloppage in heel fit.
Easy solution is stick-on Moleskin or Molefoam in the Dr. Scholl's section. The latter is thicker, but will get thinner as it breaks in, both can be stacked if more thickness is needed.
Put your boot on carefully at first until they adhere better from constant foot pressure, or you'll peel the patch off. They will wear out, just replace or stack a new one on top of the old one.
Wool should not cause an issue with temperature, works better than cotton ("the fabric of death" in cold weather and foot rot in warm), but thickness and weave might contribute.
Some PhD socks from Smartwool are densely woven and the density varies by foot zone to allow cooling in the arch. If they make tall enough ones they would be great for MC. I like wool REI hiking socks in my CBT, I'm a sales-rack opportunist so they didn't sting that much.
Quate, Crepa, Rota