There is no way -at least that I know of- to insert javascript without a shortcode in Hugo.
If this is something you want to use on selected posts and not on every single one, you can make an empty shortcode, call it in the single.html template and then insert whatever script you need in a Markdown file within the empty shortcode’s brackets.
@zeakey Code blocks are supported in markdown with blackfriday but writing executable code is something different. This is something you’ll probably want to do at the templating layer…if for no other reason than separation of concerns is a sound engineering principle. Check out the safeJS templating function in the docs.