You’re totally right - WiFi.listen() will block the main user loop.
You could setup a interrupt routine that is called from a timer, which checks WiFi.listening() to know if the system is listening or not.
To exit listening, as a quick hack, you could set WLAN_SERIAL_CONFIG_DONE to 1 to cause WiFi.listening() to exit. But please keep in mind that access to internal variables will be replaced by an API in future versions.
Hope that helps! 