I don't think it's really fair to make any assumptions yet. All we know is that an SDK is coming. We don't know who it will be available to (specially selected/approved companies? Everyone?), we don't know how apps will be installed (from iPhone interface, through new iTunes revision, etc), and we don't know how the apps will run (completely native, inside some kind of offline sandbox like current Safari-based apps).
Until we can answer some of these questions, I don't think Jailbroken apps will go anywhere. I STILL think that even if the SDK is open to all comers, the iPhone Dev folks will still be hacking away. Speaking from a coding standpoint, I highly doubt ANY SDK released by Apple will include the methods/calls that the Dev team is using for their unlocks. They won't be going anywhere.