Scott,
it is indeed possibile to disable your PC from looking at the secondary hard disk during the boot up phase and later, but you should open your computer case and then disconnect the IDE clable (usually is flat, grey and with a red stripe on one side) that connects your motherboard to your hard disk. You should be careful because cables of the same kind connect also the primary hard disk and the CD-ROM reader. However, if you can read the label on the back of the hard disk, it should be easy to identify the cable that you should disconnect.
Email me if you have more doubts or questions.