Just to clear up the FUD, the Type-C connector supports 'Alternate Modes.' This allows manufactures to implement chips that can MUX different signal types onto the USB cable SS lanes. There are 4 SS lanes that can be reassigned and either 2 or 5 additional wires that can also be used depending on if it's a cable or dock connection.
So, can the Type-C connector support Thunderbolt? Yes. Does the Type-C connector currently support Thunderbolt? No. Will someone add Thunderbolt over Type-C? Maybe.
I've only heard of PCIe over Type-C (via the spec docs) and DP over Type-C (from the VESA guys).
It certainly sounds like an excellent connector. If Apple can shoehorn Thunderbolt into that, it would be great. If they can't, it sounds like it's well worth it anyway.
That's hardly unique to this situation though. It doesn't support Firewire or eSATA or VGA or ethernet or AppleTalk or Centronics parallel either. Life moves on, and this is hardly a company gripped by concerns for backwards compatibility.
You seem to have confused "Is this the end of Thunderbolt as well?" with "I hate Apple forever for changing things." It's a simple question with a simple answer. (Yes.)
Supporting something like Thunderbolt is nice, but not exactly the same. It's not about "brand identity," it's about "does this equipment I have work with this machine?"