[Q]

Sorry Geoschmo but for me this is a feature not a bug because I am convinced MM wanted it to be this way. If even a destroyed master computer would protect a ship against allegiance subverter, would you still choose the psychic trait for 1500 racial points??
I wouldn't.

If you really can't tolerate that your super starbases are converted, give the hull a master computer ability! Then it can't be destroyed and will be completely protected from the allegiance subverter.