Of course it can, and so can the 5D Mark II. Curtis was looking among the custom functions for this, but more and more flash related functions have moved into the flash control menu, something which started with the 1D Mark III, and has become more elaborate since then.
So the setting for disabling the flash, but keeping the AF assist beam, is under the flash control menu. Controlling the AF assist beam itself may still be in a custom function in the 5D Mark II, though.
Correct, 5D Mk II Flash Firing "enable/disable" is the last item in the camera flash menu and you have to scroll down below "Wireless Set" to see it.
The 580EX II AF-assist beam firing "enabled/disabled" is C.Fn 8 in the flash Custom Function menu


