I agree with Wyck’s comment. If I can upload files, game over. If I couldn’t upload to mu-plugins chances are that I could upload, and overwrite, the theme’s functions.php or Core files instead. Any of those options work as well or better than a mu-plugin file would.
The “also modify the database” part is irrelevant because if I can upload files modifying the database is trivial. Just run wp_insert_user or use $wpdb to run SQL to directly alter the database.
In other words, if I can upload files to the server I have already got more substantial control over the server than PHP is able to deal with, more control than PHP is able to put up a barrier against. The ability to upload to the server is a very substantial hack.
I don’t know that activating plugins is so much security as it is convenience. The user can switch plugins on and off, and the developer can use activation and deactivation hooks to run special purpose code.
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