So no, the fear was not only of a voided warranty.
I don't recall Apple ever mentioning jailbreaking, let alone threatening that it was a criminal act. During the initial iPhone announcement there was talk about the supposed dangers of letting any particular app free on AT&Ts mobile network, but since then I can't recall a time when either a phone manufacturer or a service provider has said anything about the legality of jailbreaking, SEEM editing, etc.
I had misunderstood the concern being the distribution of modified, Apple owned software (similar to the Psystar case), but this appears to be a system which patches the software in place, without requiring redistribution of Apple IP.
It'd simply be the digital equivalent of the stickers that indicate if a unit has been opened or exposed to moisture.
Apple's "it's a crime" talk is to scare casual users away from jailbreaking to get pirated software. But they know that experienced users, the ones that write the apps that draw the inexperienced users to the platform, want to jailbreak. And, those users want a warranty. And, they don't want to piss off those users, many of whom have hardware-review blogs.
So my guess is that Apple is not going to void warranties for jailbreaking. If they start doing that, it's going to be really good for Android and really bad for Apple.