This is true, of course, and I understand why some companies don't want to take the risk. But I would hope that Let's Encrypt would take the opposite stance.

This is true, of course, and I understand why some companies don't want to take the risk. But I would hope that Let's Encrypt would take the opposite stance. They were born out of the EFF and have EFF & ACLU board members! These orgs live for this type of legal fight.