The Dashboard allows you to remove a repository from Tower's list of managed repositories - and optionally delete its files from your disk.
Make sure the Dashboard view is currently open.
Either select the repository you want to delete and click the "minus" button on the bottom of the list or right-click the repository and select "Delete <repository name>".
In the following dialog you can choose if you just want to remove the repository from Tower's list of managed repositories or if, additionally, you want to delete the associated files from your disk, too.