I haven't read the warranty, but what does it say about tampering with the device - does it differentiate between hardware and software/firmware? If the software/firmware is tampered with - ie. hacked - I'd expect the warranty to be void so yes, they probably can do this, particularly as they're not forcing the users to update.

Apple are not obliged to support unsupported hacks, and since they gave fair warning that the new update may cause problems on hacked phones I think they covered themselves adequately. Some criticism of Apple may have been warranted if they had given no warning at all, but as they did so I don't have a problem with their approach.