Yes, most programs should disallow W|X by default. But trying to banish the entire practice with a mount flag, knowing full well few people will go that far to run a W|X application, is bad practice. I'd rather see this as another specialty chmod flag ala SUID, SGID, etc. Or something along those lines. One shouldn't have to enable filesystem-wide W|X just to run one application.
The thing is, when you actually do need W|X, there is no simple workaround. Many emulators and JITs need to be able to dynamically recompile instructions to native machine code to achieve acceptable performance (emulating a 3GHz processor is just not going to happen with an interpreter.) For a particularly busy dynamic recompiler, having to constantly call mprotect to toggle the page flags between W!X and X!W will impact performance too greatly, since that is a syscall requiring a kernel-level transition.
We also have app stores banning the use of this technique as well. This is a very troubling trend lately; it is throwing the baby out with the bathwater.
EDIT: tj responded to me on Twitter: "the per-mountpoint idea is just an initial method; it'll be refined as time goes on. i think per-binary w^x is in the pipeline." -- that will not only resolve my concerns, but in fact would be my ideal design to balance security and performance.