I use it in lectures all the time and the mute button has never failed me. Even if you accidentally tap on words that are associated with recordings, the pen will not make noise unless you specifically hit the unmute button (which is on the bottom right of the page and virtually impossible to hit accidentally).
You could mute the sound on the pen. Just be careful of where you are writing and try to avoid tapping places where it was recording while you were writing. Muting the sound does not affect the pen's recording ability.