Just looking at the bombardment reputation penalties, I personally don't see a problem with the asymmetry. There are plenty other parts of the game which have NPC/player asymmetry. I mean, its not fair the Hegemony starts with hundreds of ships, while you start with a frigate at the beginning of the game.
Look at this way, if any time an NPC faction starts attacking you, all the other NPC factions start hating that particular faction, its going to make your game really easy, since its always going to be the Player + all but one NPC factions versus 1 faction. I don't think that is the intent.
Presumably, if the player could just waltz in and bomb every hegemony planet with their super fleet, the Hegemony would be down and out quickly, as in some sense there is no timer on the player's choice to bomb planets. I'm guessing by giving serious repercussions to the player for it, they have to be really sure and ready for those repercussions (preemptive diplomacy perhaps?), before they go on that massive bombing campaign.
As far as in game logic, I'm sorta surprised if you found a colony outside the jurisdiction of all the major factions (i.e. you're not working for any one of them) you don't immediately drop to pirate status with all of them. You've essentially become a new upstart faction which none of them logically should want to put up with. None of the base game factions are what I'd call particularly nice. They put up with you as an independent trader/explorer/bounty hunter because you're effectively making them richer every time you trade or buy something from them. This is why buying legal goods off the black market upsets them - they're not getting their cut, so why should they put up with you?
In the case of an independent colony, now there's all this trade they are not getting their cut from, and you're not protected by the current balance of power between factions.