A lot of the benefit of the rpi is the built in IO. Would the rpi still be cost effective without it? Not for many of the IoT projects that make the rpi so popular.
I didn't propose replacing the GPIO, or the camera port, or the other display port. I'm talking specifically about the other ports around the sides of the device, which are already used for more traditional computer-y things. Of course the Pi needs to retain its built-in low-level I/O, but it has another side to it too, and that's the side I'm talking about using Thunderbolt with.
A RasPi-compatible USB GPIO breakout adapter would be a cool product.