I had this problem after I had installed gpg through Homebrew first, and then uninstalled it to use MacGPG instead.
I solved it by going to Sourcetree > Preferences > Advanced, then for GPG Program I clicked Browse and selected /usr/local/MacGPG2/bin. After that, I was able to enable GPG signing on a repository.
Turns out I had installed GPG tools, it said it had a key in the control panel thingy so I figured it was cool beans... but it turns out I didn't have a private key yet. So I clicked new, entered a password, jigged my mouse and keyboard some and it all came good.
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