The Full Screen option in apps on Lion/Mountain Lion is great for maximising screen space unless you run two monitors, at which point the second one just shows a useless texture. Is there a way to get full screen apps on the main monitor and still use the second monitor for displaying other apps?
Many users have complained about Apple's Full Screen Apps "functionality" behaving exactly as you've described. I haven't seen anything stating that Apple - which is aware of this - is doing anything about it. I wouldn't hold my breath. Sorry.
This appleinsider article discusses the issue in more detail and pretty much sums it up as no.