Is there a way to disable a disk or disk controller before OSX boots?
A simple solution since you are booting off a USB/Recovery disk, you could mount the drive in "read only" via diskutil:

diskutil mountDisk readOnly /dev/diskX


Now, if your USB/Recovery disk has already mounted it when it loads, you will have to unmount it first:

diskutil unmountDisk /dev/diskX


diskX is the drive identifier of the disk you are attempting to (un)mount.  You can find it by issuing the command diskutil list and finding the drive you are interested in.

From the manpage:


  Mount a single volume.  If readOnly is specified, then the file system
  is mounted read-only, even if the volume's underlying file system
  and/or device and/or media supports writing; even the super-user may
  not write to it; this is the same as the rdonly option to mount (8). 
  If a -mountPoint is specified, then that path, rather than the
  standard path of /Volumes/VolumeName, will be used as the view into
  the volume file content; a directory at that path must already exist.