"Ctrl+Alt" appears to be a hardcoded default to grab/release focus from the host OS, which makes many common key combos in the guest impossible (without the "Send Ley" workaround menu. I've used "Ctrl+Alt+Shift" in VMware for quite a while -- would be very nice if virt-manager's hotkey combo was configurable as well. Ctrl-Alt-Backspace, Ctrl-Alt-ArrowKey, etc.
The grab combo is defined by the GTK-VNC widget, so re-assigning the component.
A similar RFE has been made against Vinagre also using GTK-VNC http://bugzilla.gnome.org/show_bug.cgi?id=501164
Adding FutureFeature keyword to RFE's.
Triage here -- looks like this has been fixed upstream according to the bug report linked in the previous comment. Closing.