Marie-Galante is already decivilized at the start of the game. Perinthus is (well, was) pirate, and pirates don't [re]colonize. Both are bad enough that a different faction might not otherwise pick them up. (I forget if DME has also applied the do-not-colonize tags to Marie-Galante)
Also, is it possible to get some tweaks to the reputation system to make it a bit less... silly at times? Transponders are a pretty big one, even factions who are Welcoming, Friendly, and even Cooperative still get pissy about transponders even if you're "well known across the faction" and are willing to go to war over it. No diplomatic immunity if you're an established faction, no ignoring the violation if you're friendly to them, no bribing them to look the other way, and they'll still bother you even if you're clearly an invasion fleet looking to gobble up any flounders that wander near you on your way to invade their world while running dark (Really, pickets should maintain contact on much larger fleets if their transponders are off rather than suicide diving to ask them about their license plates).
I found a way to mess with the rep penalty for being caught with your transponder off, so I might well remove it in a future version. It's the most annoying part of the mechanic, especially if it happens to push you over the hostile threshold.
Sadly I don't have a way to change the behavior of patrol fleets regarding the 'bother a huge fleet which realistically should be presumed hostile' behavior (here's an interesting post/thread on a related topic, at least).
Similar case with Colony creation, if a faction is "Cooperative" and you're benefiting from trade concessions, that ought to cover establishing a colony in their systems and probably shouldn't ever do expeditions on your faction. It's kinda like if Britian sent in a team to sabotage or capture the industries of a france principality, it just doesn't make sense to do so given the political climate. Or if Germany attacked a US military base inside of their borders, just doesn't make a lot of sense.
For a colony in their system, just pay the tribute when the demand is made, or have an alliance with the system owner.
Expeditions in general are vanilla (and a placeholder mechanic, I assume) but Nex already lets you turn them off! enablePunitiveExpeditions in exerelin_config.json
I've considered making that setting default off since expeditions are a really daft concept in a bunch of ways, but I dunno if I want to outright remove features from the base game.
Maybe worth looking at Saturation Bombings too, the AI factions don't seem to care reputation wise if it happens between two AIs, but if the player does it you get into a hot war with everyone. Realistically, it should have a more gradual curve. Allies of the faction that got bombed should get a pretty sizable loss in reputation (let's say 30-40) with you, neutrals to the faction that got bombed lose maybe like 20 reputation with you, and enemies lose maybe 10 reputation with you if any at all. It should also apply to AI factions as it's kinda weird that factions will saturation bomb each other and that seems to matter less to the political climate of the system than a jilted wedding arrangement.
If sat bombing by NPC factions had reputation penalties, I'd need a way for the faction to figure out whether it was actually worth doing so. The upcoming strategic AI could do just that (so I might implement this at that time), but it's likely the answer (compared to alternative actions by the faction) would be 'never'. Which, to be fair, is also often the case for player.
That said, the asymmetry here with player getting punished when NPCs don't is exactly why there's an allowNPCSatBomb setting in the config file 
As for player's rep penalties, there are currently a few cases where the impact is reduced: a third party faction is vengeful to the target; the target faction has the Monstrous trait; or the planet/station is small (size 3 or lower) and/or outside the core worlds.
Other than that, well, if you mass-murder a hundred thousand or a million civilians in an already decaying sector, don't expect other factions to approve of this 
(Insta-hostile is an unlikely response, insta-suspicious or inhospitable with a large numerical penalty to push already-neutral factions into hostile territory would be more likely. All the same, I don't have a particular reason to change this right now, especially when a remarkably large number of players in the community are apparently still perfectly happy to sat bomb Hegemony and others for comparatively minor offences)
Yeah, the tribute is fine though it has a couple of issues with it. Namely if you conquer a colony, no tribute is necessary so it's almost always preferable to conquer someone compared to trying to cohabitate (or do shenanigans where you give it to a faction you're hostile to and conquer it later like you're planting crops). Second, as far as I know it's the same amount of tribute regardless of how friendly or not you are with the faction, so long as you're not outright hostile? Guess the other issue is that systems will still be "claimed" by other factions, even if they own like a single pirate outpost and you control the other four colonies in the star system.
On the saturation bombardment topic though no faction as far as I know are ever vengeful with pirates or luddic path, so if you wanna nuke them everyone will hate you for it, despite everyone being hostile to those factions with a couple of exceptions. There's also the thing that, for the most part, it's just much easier to just repeatedly raid the industries over and over and over again as it gives no major penalties aside from just needing the marines and a couple in game days to go and sang bag their industries till they're -30 or more instability. That's more of a vanilla issue though. I guess in general the saturation bombardment being so punitive relative to you know, invading worlds so hard that they decivilize entirely or mass invading the entire sector like the space mongols is a far healthier for your reputation, especially given that other factions also use saturation bombardment fairly regularly.
