You had better have the civilians check what their parent race thinks of the contact race. (Use the alien race status of the tactical intelligence screen).
Otherwise in a game with multiple races in the home system, the civilians will be running all the time. This is what is happening in my 4.0 game.
By the way, this would be a nice check for interrupts. Only break on hostile contacts. That way my multiple Sol system can have friendly and neutral races and not stop on every sub-pulse because of a new contact.
It would also be nice if a passive contact that had an active transponder would be judged the same way. When the civilians get close enough to earth to become a passive contact, there is no need to break the sub-pulses either. This could make using active transponders a postive thing in allied systems.