Yes, you can use your audio channel.
You have to consider its frequency response: (theoretical Maximum of 20kHz?)
You also have to buffer the audio output. Use an opamp as a buffer for that. You do not want to overload your audio jack.
You will run into challenges of how "Fast" you can send data to your audio channel. But I think it is possible.
Another way is to use a good old parallel port, IF you have one :). Those are nice to command some electronics.