Replacing their (few) Kindles for free regardless of the cause of the damage, would be less expensive than paying all those programmers full-time salaries to "protect" Kindles from jailbreaking.
How many people do you think it takes to do this? At least a couple.
How many Kindles do you think brick because of third-party mods? Not many, they are tried and tested. Maybe 100 per year? (Personally I think I am vastly overestimating...)
Full-time salary for a couple new people: lots of money. We're talking in the range of hundreds of thousands of $'s.
Cost of 100 replacement Kindles: not much, in the grand scheme of things. Ten grand, tops.
It's even cheaper if you assume I was off by a factor of x10.
Solution -- don't stop supporting those problems. They won't stop anyway, it costs more time to
check than is worth to simply replace it no questions asked.
Customer service remains wonderful.