You may or may not run into problems with just swapping the drives, I don't really know. I've never tried it, nor have I ever heard of anyone trying it. But, there's a couple of things that you're going to need to look into (or find out the hard way after opening both of them up):
-Are both drives the same interface standard? Some new optical drives (including, I think, some slim drives) are running off a SATA interface. It wouldn't be implausible for Apple to have switched from IDE to SATA when they swapped to PC hardware...
-What about firmware? There are some desktop PC drives that will drop right in and work on a Mac (a bunch of Lite-Ons, various Pioneers, etc.) but I'm not sure how a drive that was set up to boot on an Open Firmware system will deal with talking to an EFI system... there's a good chance that it could work just fine, but there's a chance that it may just refuse to talk to the drive.
Have you looked around to see if anyone has tried this before?