Just to make sure this goes down as answered, I want to put down what David Jacquel said in his comments:
File folders for themes are stored in _includes/themes
and assets/themes
.
Delete these and your unwanted themes will be gone.
A second option for removal, which I'm not positive about, is to run the reverse of what you did to install, in your case: rake theme:uninstall git="https://github.com/jekyllbootstrap/theme-the-program.git"
. For others, it might be gem uninstall [theme-gem-name]
if you installed the theme that way.