You can use file permissions instead of the read-only attribute if you want to stop things being deleted.
Making it so only elevated processes/accounts can modify/delete the files is often good, since it means you can still make changes fairly easily but most software, and you most of the time, cannot do it by accident. (Assuming UAC is being used normally, of course.)
For files + folders: Paste empty file list
For just the folders: Recreate Empty Directory Structure
But that is a separate topic, so please start a new thread if you want more help in that direction.