Fear of crowds at MP might be overblown; my daughter and I visited in early December two years ago, and the only time we ever felt part of a "crowd" was on the bus from Aguas Calientes to MP itself.

The town of Aguas Calientes didn't feel crowded at all, just a normal town. Cuzco was a bustling busy city but easy to get around and not nightmarishly crowded.

If you're looking for an entirely rural experience, without tourists, then sure, avoid MP and Cuzco. But don't elevate either to the status of a tourist trap or Disneyland sort of place. They're not. Their uniqueness and the reasons to visit are not, in my opinion, spoiled by big crowds. My opinion, your mileage may vary.