Flying a lot on EU1 i have never been shot by friendly AA missiles.
Most of the time no Missile Specialist even carries AA, most go for AT (which is a problem in itself). And even if the AO is completed (red circle is gone) there might still be enemy AA soldiers/vehicles down there for a few seconds.
Don`t get me wrong this could still happen, i have been shot at by a lot of things by now, but friendly AA is so rare that i can`t remember this happening at least once right now, neither to me nor others when i was online.