Change the preference "Automatically lock objects added to workspace" to also make the files read-only in the CAD session. The lock objects in the workspace is very ineffective because the only consequence of setting it is a warning box that pops up telling the user that the file is read-only in the workspace, which when they press OK modifies it anyway. That is barely different from the popup to check out the object. In both cases they end up with a modified object in the workspace that is probably released and cannot be checked in.
If the CAD was made read-only in the CAD session it tries to prevent the problem at its source. The CAD software would not be trying to save over the files in the first place. For instance saving an assembly often tries to save the dependents, and would be prevented by a read-only setting. If the user tries to save over the file, the save as dialog will appear trying to force them to save it as something else.