Is it possible to intercept the audio data of voice call in Android?
You can record all Microphone audio using the Google API with your own software. Also - note that not all Android phones allow to capture incoming audio because of hardware limitations.

It will be better if your create your own Native application and use VoiP for your outbound audio, which is easily achieved because there are many VoiP application out there.

You cannot bypass the Google API because the driver level is protected by the Operating System. You application only has access to the API that the OS exposes to you. So if there is no API similar to "RedirectMIcrophoneToAuxAndThenToGSM" - then sorry you cannot do it- even using Native Java code.

Alternatives


Get Android source code and make the changes you need. Compile it and programme the devices yourself. This is not an easy task for end users and would normally be done on company phones. This is great because users cannot turn of the encryption stream you are trying to force because you control the API!
Make your own android phone device or get a Chinese factory to make one for you with a custom GSM encrypted/decrypted module. Hardware encryption is allot faster


I think the sole reason why NO phones allow you to replace the outgoing GSM audio with a altered one is it most likely illegal. TO prevent voice masking in terror, bullying, extortion, black mail,etc ...

Since you have a legitamate reason to encrypt your voice that must mean there is high financial benefit involved- So inherently you must make your own device to do it.