>Do you really need jquery. Force people to use vanilla javascript and don't let them put their js on head section.
This would break almost every existing plugin and theme.
There is also a petition to remove jQuery from the core, which is a more reasonable direction: https://petitions.classicpress.net/posts/187/jquery-to-vanilla-js
Why force people to use Vanilla JavaScript? That smacks of WordPress's "decisions not options" philosophy which doesn't apply to ClassicPress.
In any case, they can always load jQuery themselves in a theme or plugin. And trying to prevent people putting scripts in the head section will just make them use script tags in their theme HTML instead of the proper enqueuing functions.