Impossible deactivate the disk
By typing the command lsof /Volumes/Mac\ HD\ 2 into the terminal, you can get a list of which apps are using that volume. The output looks like this:



The COMMAND column should tell you what's using your disk, and what you have to quit.

Based on your comment, it looks like the GitHub application is using your disk. Try quitting it first, then you should be able to do it.

In general, you can also use Recovery HD to safely perform disk operations without having open files spoil the fun. It has Disk Utility and you can eject the partitions that normally run OS X and have your way with them.