I think that the issue with this asymmetry stems from the fact that it is rooted in politics and realistic, but in real political situations this is just as unfair. Placing it in the game doesn't change that. Sort of how the big factions agreed to hate the pirates, so you can do anything to pirates, since nobody cares about them - and unless you make somebody care about you, prepare yourself to face the same fate. Maybe. I can imagine that, against the player flying around and making their own empire with blackjack and hookers, they would send only limited force at first, to scout the situation and to avoid giving someone else advantage over them.
It would be nice if this initial situation resolved differently, depending on what player is doing. Unimportant colony would only result in pirate raids, but a bigger one would attract skirmishes with other factions before raids, giving the player time to react. If the player has a commission, however, the commissioner could simply share intel way before the raid, or harass that force themselves, weakening it enough the player doesn't have to react. Of course, any of the factions growing in power upsets the balance, that can easily lead to some nasty things, like war...