I don't know anything about how to do it with AVFoundation (or if it's possible, or if you're already doing this), but to some approximation depending upon codecs, you can make a lossless recode of the video. E.g., what Rogue Amoeba's Fission does, but for both video and audio.

You could also provide a way to export a list of cut points suitable for feeding to some other workflow. E.g., ffmpeg.

These may go beyond the simplicity and spirit of your app, which seems very nice.