I've been working on a balloon controller as well, although mine is incredibly bare-bones [1]. It only reports position, altitude, and temperature; but since it's so minimal it only weighs around 2 grams.

For your use case, you might want to consider a small external microcontroller that handles TNC functionality, this /might/ be smaller and more lightweight than a USB sound card.

Your payload controller software looks pretty awesome--nearly makes me want to launch a balloon with a full Linux single-board computer!

[1] http://protofusion.org/wordpress/2015/10/featherhab-2-gram-h...