I'm sure they can find work arounds.
And on the other side I thought of how AMD could throttle/handicap nVidia cards on AMD boards without removing PCIE at all.
This would be an illegal practice and they would go bankrupt. Unlike Intel who recently had to pay out quite a hefty fine to AMD, AMD could not take such a blow and they would fold in the wake of the massive litigation to follow that.
Nvidia can argue that they must block the code from running because otherwise AMD or people using their cards could trick the code into running on another GPU. Which is true, as it was being done before.
The answer is not to fight back - AMD has zero clout with Nvidia. The answer is to compete. Release, support, and push another standard of physics processing to developers. Developers chose to use PhysX because they essentially get a lot of support to include it in their product. AMD has a bit of history of not really supporting developers. This has caused issues where Nvidia has AA in a game, but AMD does not - because Nvidia sent a team of programmers to hack in some AA optimizations and afterward everyone wants to cry that they should share.
You really have only two choices if you don't like it.
Choice one: get angry and don't purchase Nvidia products (which if you're unhappy the chances are that you already do not do so)
Choice two: do something to help push an open standard of physics processing, or join the industry and help AMD to create a competitive product.
There really is no choice three convince amd to illegally handicap competitors products.
Or post about a silly hypothetical situation on Anandtech, because you are frustrated, comparing apples to oranges.