I'm guessing the best way to do this would be to add something to $PAGE->requires to specify extra head entries (maybe $PAGE->requires->head($tag, $contents, $attributes)?), and then modify page_requirements_manager::get_head_code to fetch those tags. This way, there won't be any modifications required for themes.
This functionality would also be helpful for, e.g. adding "prev" and "next" link tags for modules that have a defined sequence.