If you need to delete a repository physically, use the specially designed ITRepositoryRemover.exe command-line utility shipped with InTrust. (Windows tools do not let you delete a repository easily.)
The utility resides in <InTrust_installation_folder>\Server\InTrust.
Before you run the repository removal utility, remove the repository from the InTrust configuration. For that, delete it in InTrust Manager or InTrust Deployment Manager.
You may have to wait until the repository services to stop working with the repository and unlock all the locked files in it. How long you need to wait depends on the repository size and how many other repositories there are.