Why did Clovis toolmakers choose difficult quartz crystal?

Good job neither the article nor the backing paper discussed made any such claim.

Perhaps you're confusing

  "which may have had symbolic or ritual significance."

with "religion"?

This is what I would bet on. If you spent decades of your life knapping various "easy" and ideal stones for tools and getting quite skilled at it, it doesn't seem like much of a stretch for them to try knapping a "difficult" stone just because it looks cooler and you can show it off.