I looked into this some today, it looks like it might be possible to create a new class to replace acf_input, then reassign acf()->input to use the new class. This should allow you to replace acf_input::save_post().
This is more invasive and hacky than I’d like, but it might work. It would be better to just have this functionality built into the core, of course. I wonder if Elliot would consider it as a feature request?