When APC cache is full, it hangs Apache. Apache responds to requests, however waits forever for APC cache to free some resources, but this will never happen.
I run every 10 minutes CRON job with my own small expunge script, which deletes expired entries from APC. Ok, I could add more memory to APC and/or I could run the expunge script more often. But that's not real solution, I am looking for some new way how to deal with issue.
It's not really the final solution, but I have written small PHP APC expunge script that I had proposed in my question. This script is run by CRON every 10 minutes and it manually removes expired items. It's far not perfect solution, but at least it helps a lot.
I am though still looking for final solution.