I've finally got round to checking the contents of files also, when comparing directories. It's done in a separate thread, so larger files shouldn't block the application.
When comparing directories, you can update or delete files. As a verification, you need to switch one or both locations from "Read-only" to "Modify" with the buttons in the upper right corner. And the SHFileOperation calls will ask their default verification also.
So if you still over-write important data by mistake, it's your mistake. (And you should consider taking backups and using a version control system.)