The way Apple has implemented Thunderbolt, it encapsulates a display port signal for video. There are two routes Apple could go for a Mac Pro and still provide video over Thunderbolt
The first is the software solution requiring driver support from AMD and nVidia to tunnel the discrete GPU's video signal through PCI-E to the Thunderbolt controller. Similarly the Thunderbolt controller would also have to pass various display information back to the discrete GPU. Due to the overwhelming combinations of video cards, drivers and motherboards, getting this solution to reliably work on the Windows side is next to improbable. On the OS X side, much more feasible due to Apple's narrow selection of components and their control of the software stack but still challenging to develop.
The second solution would be to add a Thunderbolt controller and a PCI-E-to-PCI-E bridge chip to a discrete graphics card. This would eliminate the PCI-E tunneling for the video output as the GPU's DisplayPort signals can be wired directly into the Thunderbolt controller. Now there is a bit of software support required for the PCI-E-to-PCI-E bridge but this is rather straight forward. The downside is that this would require specialized hardware (IE more expensive) from AMD and nVidia. In fact, it'd be reasonable to assume that AMD or nVidia wouldn't be the board designer for the video card as AMD and nVidia have no love for proprietary Intel technology. If Apple wouldn't develop such a card in-house, they'd inquire with various board partners like ASUS to design the board for Apple at a premium.
Lastly, there is the option to merely allow data over Thunderbolt on the Mac Pro's. This would make the extra functionality on Apple's 27" Thunderbolt display useless on such a Mac Pro so this solution is highly unlikely.
