When I tried to remove this deployment, the IDE deleted everything in my desktop directory.
!!! Damn that bug, we fixed this in 3.8.4 QF#2 because someone else tried to do this with horrible side effects (what you just had happen). Is everything OK with your computer?
Any suggestions on how to manually delete the deployment?
Yes, never never never deploy a Custom Location deployment to an existing directory, always deploy it to a new dir, like C:\mynewdeployment, that way when you need to remove it, it will just erase that dir. This is the check we added for QF2 to protect people from deploying to C:\ or their Desktop.