As far as I remember, as soon as the helm gets even partially damaged the pilot will stop piloting to repair - or did they think of that and allowed him a partial bonus, like the one you still get even if the pilot is engaged in hand-to-hand?
Even if he can pilot the ship at a reduction while repairing a partially damaged helm, late game if something gets through your shields and hits the helm, it's usually going to be a missile, and they'll generally do more than one point of system damage. At least if you only have level 1 piloting you will be done with the repairs very quickly, regardless of the size of the missile that hit it.