Thunderbolt will stick around on the Pro models for a while, but I sense that eventually, it's going to "go the way of firewire" -- that is, to be superseded (not totally) by future iterations of ultra-high-speed USB.
I realize that USB may not have the potential to provide all the advantages of thunderbolt's pci-e connection, BUT, Apple may just decide that not enough users actually -use- such capabilities to justify keeping it in future models -- particularly when they seem obsessed with "making it thinner".
Then again, future re-designs of USB may surprise us with its capabilities -- just as the inclusion of "UASP" into USB3 totally revamped how USB transfers are conducted "on the bus" (USB attached SCSI protocol relieves the CPU of most of the burdens it previously carried under USB2).
Thunderbolt will probably be retained on the Mac Pro line for the longest. Perhaps even on the Mini, as well.
But I predict it will disappear sooner-than-expected on the Macbooks.
No infallible crystal ball here.
I could be wrong...