First off, it's not abundantly clear that the onboard video is what is causing the problem. I'd say that's not a bad guess, but at this point it's still just a guess. Did you look through the other thread?
Second, I scanned your manual and couldn't find anything in the BIOS to directly disable the onboard video. It's a pretty hefty manual, did you see anything in there? For all we know right now, maybe you don't do it in the BIOS. It could be a jumper. It could be downright impossible. I'd recommend you search the manual thoroughly to be sure. I don't mind scrolling through a manual for someone else but I draw the line at having to read the whole doggone thing.
There are lots of reasons why hibernation might be slow. It might be a RAM problem, a USB device taking forever to snap to it, or whatever.
are you using for the ATi card? Does the old video device still show up in Device Manager? If it does, have you tried disabling it?