Problem: You have to babysit colonies. Even if the frequency of the attacks is reduced in future updates, it will still interrupt your exploration, trade, whatever you had going on.
Solution: A way to get your character immediately to a colony when it is attacked. Maybe you can just remote control a secondary stored fleet. Either at any time, or only via relay. That fleet can't leave the system as long as it is remote controlled.
Your original fleet just chills while you are "away", maybe at reduced maintenance.