How to stop wp-editor() overwriting my HTML?

If you were always writing in HTML, you could add the following to your functions.php file:

remove_filter( 'the_content', 'wpautop' );
remove_filter( 'the_excerpt', 'wpautop' );

I do this for some of my own sites.

As it sounds like you want the option to turn this on or off, you may want to try the wpautop control plugin.

This should let you turn it off on your posts, while leaving it on for other users.