Deleting a file using tortoisesvn repo browser does not cause any existing files to be deleted from the windows directory containing the repository. In fact it adds 2 files - the record that the file was deleted and the comments associated with that record (ok, I simplified).
However, making any change on the repository requires the ability for the server to delete files from the windows directory containing the repository. Changes are first recorded in a new transaction file, then the repository is modified according to the transaction, then transaction file is deleted. This happens on every change, even if you're just changing a comment in a file. Preventing normal file operations in the repository's directory is going to corrupt the repository.
There is no functional difference between using tortoise svn to delete a file, and checking out a working copy, deleting the file, and committing the result. All required permissions and structural changes are identical. All the same hooks get fired in the same order and they get the same information. Both record a revision saying the file was deleted, and that revision can be reverted in both cases. You can't separate the activities. If you prevent one, you prevent the other.