Other languages achieve a good compromise by clustering data structures into fewer parts with only a handful of mutexes that are locked while other threads work on different datasets. This is usually done manually and with great care as it is the heart of both safety and performance. I don't know if there is an automatic solution to this problem that is compatible with the way python programs are structured.
The libraries basically assume that, while you call them, nothing else changes. In order to ensure that you need to lock everything down. Because you don't know what these libraries do and what data they access it needs to be everything (like it is today). It should be possible to only lock the GIL when such a library is called, so there should be kind of a middle way forward.