This why we need common protocol for communication which could even enable cross platform communication and avoid problems like these. It's not like this is something radical, IM clients had common protocol like XMPP before the companies started to lock-in their users within their platform.
Anyways for this particular problem, it might be possible to for a service to monitor mic/webcam usage and take an action when we receive another call from different application; But a permanent solution would be to use a common protocol at least for setting the status/send engaged tone when in another call like we do in GSM as there will be always a new VoIP app.