Permanently Disable/Ignore Secondary Disk?
Yes!

First get the UUID of the partition you want to prevent from mounting...  You can get this in Disk Utility "Get Info".

Now open your /etc/fstab file for editing:

sudo pico /etc/fstab


In this file add the following line (use your own UUID naturally):

UUID=[your UUID] none hfs rw,noauto 0 0


And save the file.

Restart for the change to take affect.

You can always mount it manually in Disk Utility.