How can I disable the 2nd hard drive in my 27" iMac?
I don't know if it'll work, but try going into the Energy Saver section of System Preferences and select "Put hard disk(s) to sleep whenever possible". Then go into Disk Utility and unmount the hard drive. With no way to access the drive, I would assume Mac OS X would put the drive to sleep.

This is a temporary solution though, and it won't persist across reboots (Mac OS X automatically mounts all available drives at boot). If you're really not using the drive and don't have any data on there that you want, my suggestion would be to go into Disk Utility, repartition the drive, and for the format select "Free Space". Once done, Mac OS X will be unable to mount the drive and should put it to sleep.