Honestly, if I had a medical issue that required silence (or, at the very least, no music's being played), I'd be speaking up even if the orchestra hadn't asked for permission (which we haven't ruled out, to begin with). There was plenty of time before they actually started playing to say something. If I were too embarrassed or nervous to call attention to myself by saying something to the group at large, I would have confided in one of the flight attendants who could have addressed it anonymously.
But, I sure wouldn't sit there suffering if I had the chance to say something. If I did, it's my own fault.