Not sure about the composition of atmosphere at those exact altitudes on Jupiter, but aerodynamic heating was a serious concern during Cassini's close Titan flybys, and that's "just" at ~6.3km/s max. IIRC the closest one was the T-70 at 880km; a lot of work has been done to make sure it won't tumble or overheat. (Titan's low gravity makes its dense atmosphere reach very far, so 880km is really low)