Earlier quoted context omitted.
I'm not the least bit concerned about NaCl's involvement here, but I'm still deeply scared by the potential for things to go very badly in the lower levels (but not enough so that I'm willing to disregard the benefits of these APIs, mind you). What it comes down to is that current GPUs do whatever you want with no concern for security; that part depends on the driver and userspace 3d stack. This isn't necessarily bad…
Virtualisation's rise in popularity has caused IOMMUs to start showing up even in some consumer chipsets. Do you think an IOMMU and a driver that supplies it appropriately restrictive page tables for the GPU will be enough or do we realistically need GPUs with some kind of native memory protection support that can somehow be intertwined with the CPU's process model?
I think that proper protections should be put in from the hardware on up through the drivers, but it's going to take a lot of work and a lot of research to get it right.