I don't think they'll do it because the way it is now was a deliberate design decision -- mission control IS aware of multiple monitors (you can see it when you activate it), it's just that one virtual space spans across multiple monitors -- for whatever reason, they thought this would be the "right" way to do things, even though that in the REAL PHYSICAL world, those are TWO COMPLETELY DIFFERENT SPACES -- and when you try to tell apple that they're wrong, they will either ignore you, or if enough people complain, they will hold a stupid "event" and give away free stuff (antennagate ;p) -- I know I'm being calous and sarcastic..sorry, long day.
Maybe they'll change it -- the diagram is a nice touch -- maybe someone from apple will actually look at your suggestion and read this and other threads talking about the problem. But on the other hand..
Then there's other opinions out there that differ and say that the way full screen apps work now is better than how it was before:
http://osxdaily.com/2011/08/11/multiple-displays-full-screen-apps-mac-os-x-lion/
They claim that the fact you can drag an app's widgets \ panels onto the blacked out monitors areas as being the way that this is "supposed" to work -- but what widgets and panels does quick time have? The stupid play \ pause \ timeline bar? I think this only applies to programs that actually have components like that -- and anyways, I'd much rather drag them onto another monitor with other stuff on it so I can multitask, not drag it on to a black space ^_^
This is how I've worked using photoshop for years -- I drag the history window on to a second monitor and all the other little tool windows too...and then maybe I'll also keep a browser on that display as well as an IM client.
I think the whole full screen app mode is just a bad idea in general -- the stupid transition effect takes a few extra seconds to put the app into full screen "mode" and plus some times you will see the top menu bar flicker when using mission control...but -- I can see how it would be useful for some apps...That's why I think your idea is probably the best -- keep it how it is by default but add the option for others who don't want it that way to unlink multiple displays in mission control.