I know, it is outrageous. This is why I've chosen to install standard hard drive and keep my money in the pocket.
So you should realize that when you say you had to put software on just to keep the fans at bay, that it really is preposterous.
MacBook Pro - swap drives at will
Mac Pro - swap drives at will
Mac Mini - swap drives at will
iMac (pre-2009) - swap drives at will
iMac (09/10) - swap drives from same company, or swap drives and purchase specific cable
iMac 2011 - swap drives and have to install software because Apple was keen on limiting you (currently) to what they offer
I'm sure Apple later on down the road will resolve this. I'm sure enough people will complain and they will issue an EFI/system firmware update to resolve this (ie. if you have an Apple drive, it will use the new temp sensor tech, if non-Apple firmware drive is detected, it will use SMART data.) I can see a class action lawsuit due to this (people have sued for less frivolous stuff prior to this.)
Personally, I think an ideal solution would be offering a firmware updater for the hard drive (like back in the OS 9 days) where if you get a drive that Apple offers (like a WD Caviar Black) that you can just install Apple's firmware for temp sensing onto the drive. That way if you, say, reinstall OS X, or upgrade the OS, thereby not allowing OS X to run the HD/Smart Fan Control program, it won't go wind tunnel mode while you're installing it. A low level driver/firmware installer makes sense in this case, versus a software program that has to be run at startup just to keep the machine at a normal operating sound level.