Sure, if you have a rogue application on your computer, it can access the GUI of a program whose security is critical (e.g: a password manager), but even if all the GUI were isolated, you've still got a rogue program on your comp.
All the security posts I've ever read have pretty much told me that once you're running a malicious program, then it's game over, your system is owned by your adversary and the only good way to move on is to wipe the drives, and start fresh. Why then worry about GUI isolation? If the GUI is isolated, a rogue program can presumably uninstall your secure GUI server and replace it with another!
This blog mentions Qubes, which is cool and does mitigate the rogue program from what I understand, but anything short of isolating whole applications from each other at the hypervisor-level, is fussing about the wrong thing IMHO.
Then again, I'm not a security professional, so what I've said is likely all wrong...