The choice of units to display to the pilot (feet vs metres, nautical miles vs kilometres, etc) doesn't have any necessary connection with the choice of units for engineering drawings, engineering calculations (e.g. calculating forces on various components during flight), etc. You could keep the former in non-metric and do the later in metric.
Actually, many planes support displaying metres for altitude as well as feet. This is because, while most of the world uses feet for altitude, a handful of countries (China, North Korea, some ex-Soviet states) use metres instead. On an international flight, pilots can even change the units displayed on their instruments as they pass from non-metric airspace into metric airspace and vice-versa.