>First off, this is not why Python has a GIL, but lets leave that aside.
Atomic writes are more expensive than non-atomic ones, but they are not slow operations in the grand scheme of things. If you properly implement acquire-release semantics, they are not even that slow under high contention. Compare this to a GC which literally STOPS ALL THREADS, it's nothing.
This is actually part of why Python still has the GIL. A GILECTOMY was attempted and multithreaded atomic refcounting made things a lot slower (going up with the number of threads) and even other methods were not sufficient for performance.