I was waiting for the camera to stop picking up sound the whole time. It got really squeaky and full of static towards the peak but it never seemed to happen.
Sound vibrations will still be picked up in a vacuum in this case. Vibrations through the rocket body will be transmitted to the camera body (direct contact) which will then be transmitted to the microphone (again, direct contact). According to Wikipedia[1], 90% of the Earth's atmosphere, by mass, is at an altitude of 52,000 ft or lower.
[1] http://en.wikipedia.org/wiki/Atmosphere_of_Earth#Pressure_an...