Is the Thunderbolt bandwidth sufficient to run a modern GPU? AFAIK you'd only have one 10 gbit/s lane to use for it, and modern PCIe video cards use a lot more than that connecting directly to mainboards over multiple PCIe lanes...
Tests that have been done comparing the performance of relatively high end desktop cards on 1x, 4x, 8x and 16x slots have established that while there is a performance penalty, such a solution would still out perform most mobile GPUs.
http://www.techpowerup.com/reviews/AMD/HD_5870_PCI-Express_S...
http://www.techpowerup.com/reviews/NVIDIA/GTX_480_PCI-Expres...
Forgive my lack of a source, but was there not an article (maybe on Anandtech?) about high-end cards being 90%+ as performant on a 4x PCI-e slot?