Reb Elchonon Wasserman in Koveitz Shiurim (84) learns from here that whenever it is uncertain if the principle of ‘kim leih b’dirabah mineih’ applies, he would still be liable for the payment.
Reb Yitzchak Zilberstein comments that if not for Reb Elchonon, a distinction could have been made between a court-imposed death penalty and a case where one incurs death by the hands of the zealots. In a case of an uncertainty regarding a court-imposed death penalty, such as one who desecrated Shabbos in a time where it is uncertain if Shabbos has started or not (bein hashemoshos), and at the same time he burned the stalks of his fellow, he would be exempt from paying for the damages. The reason is as follows: Even though, Beis Din cannot administer the death penalty, he would be exempt from paying because he might be liable for death. However, in a case where one does not incur a death penalty; it is a transgression where zealots have a right to kill him. In a case of uncertainty, where he may not be killed, he should certainly be responsible for the monetary payments involved.