I have the original 2GHz Core Duo MacBook with SuperDrive at home. The computer provided for me at work is the Core 2 Duo version of the same machine.
My home Core Duo machine does get hotter at times, but then I also work it harder and actually use it on my lap, in bed, whatever, with stuff like Aperture, while the work MacBook is almost always on a desk and just runs web browsers and mail clients mostly. Neither one has never become so hot that it worried or bothered me, though. From what I've experienced so far I don't see any significant difference between the two when used in comparable environments under comparable workload.
For what it's worth, I previously owned a 12", 1.33 GHz PowerBook G4 and I think in terms of heat my results were about the same. Its fan did come on on occasion, while I can't recall noticing that my MacBooks have ever had a fan come on to an audible level.