I don't disagree with you.
I do, however, believe that if Apple wanted to design full-screen app mode to leave other montiors available for use (eg: not greyed out by design) then the can make this happen.
As oliver234 said above, the current behaviour is a design decision by Apple. I personally think full-screen app mode as implemented is a dumb design decision.
Was this decision driven by the fact that the bulk of Apple revenue is freom elsewhere Macintosh computers and OS X (eg: iOS devices, iTunes)? I don't know, but I am dissappointed that I cannot use full-screen app mode AND multiple monitors. Thankfully I can still maximize an application window. Hopefully Apple will leave this feature/behaviour in place.
Some third parties (eg: VLC) have designed their applicaiont to go full screen using Apple's full-screen mode OR an alternative that leaves other moitors untouched. I'll use those as I find them.
Apple can pretty much make any design decision they deem fit to "bless" become a reality as we see by Apple's product array.
It is absolutely possible that in designing full-screen app mode the way they did Apple made an error and/or miscalculation in predicting the negative effect it would have on workflow and hardware investment for a portion of users.
I cannot conjecture on how difficult/easy it might/might not be for Apple to change/re-design full-screen app behaviour more to the overwhelming preference of contributors to this thread. However, I know that if Apple wanted to they could.