I don't think checking out the document would be a solution for us. We use automated proof workflows that may have more than one user reviewing the document at one time. Also when the review is complete we move the proof to the next proofing task which would require a new version be added on top and if the last user forgot to check the document back in it wouldn't allow a new version. I think we would have more occurrences where the file being checked out became an issue than the file being accidentally deleted.
When you delete a folder in the documents area if gives you a prompt to delete the folder and keep the contents or delete it all. If you delete a portfolio it doesn't delete the projects in it too. There should be the same option when deleting a task that has files on it.