First off, this request is not the removal of the Allow Media Deletion feature. It's to add a little more security to it.
I don't know the networking jargon so please bare with me.
What I suggest is to change the way Plex Media Server can delete files from your server by limiting deletions to only on your local subnet(private subnet) from the server.
That way, you will have the benefit of deleting content you no longer want while you are sitting on your couch at home and prevent anyone else deleting your files outside of your network.
As always, click the like button on this post and leave a comment if you want to have this feature.