if you want to do this as a theme this will be your only choice. userinput (markdown)-> server side cooking in ruby → (html) retrieval by other users and possible decoration. This is the promise that will be called before hitting the save/reply button. This will not show up in drafts, but you are right it would show up if you were to edit the post. if you want to get around this you need to undo the changes that you do on save when the composer opens/switches to the post you modified before. I could go into further detail or you could just read the code and do your own experiments.
cheers! 
EDIT: I just thought about this. theoretically you could also recook on the client side. But I think thats a bad idea for performance and other reasons. Or just do a plugin: Plugin Tutorial #1 - How to manipulate the text in the composer?