I dont really understand the rationale behind expeditions working the way they currently do at all anyway. Of course colonies being attacked is certainly a good mechanic, but for other factions to simply automatically do it with out repercussion seems extremely unrealistic. They have their reasons, of course, you being market competition, or doing something that annoys their set of morals is a reason for them to not like you or want to try and do something about this upstart colony/faction, but just sending open warfleets against you seems very badly thought out.
Id expect something like this:
1. Those fleets are costly for them to do
2. If you are commissioned you are a formal part of that faction, you pay a tax, but attacking you is attacking them, if they are at war they might even send some ships to help defend your colonies. Doing things that faction approves of does not bother them (making fuel if you are part of the SD is merely expanding their monopoly on fuel production, for example)
3. With open war being diplomatically inconvenient, people who do dislike your colony have other means to try and persuade you to stop, such as economic sanctions, sabotage, attempting to start a revolution, or taking advantage of natural disaster (a food shortage sees their operatives trading food to hungry civilians in exchange for electrical wiring and machinery, thus lowering your production output). Some people within your own faction may not like you and try to do this (someone in the SD not liking some upstart getting in on the fuel business, even though you are allowed to do so officially)
4. A set of diplomatic mechanics to try and gain favor with people in your faction/other factions.
5. If you are not commissioned you count as your own faction, and have diplomatic options to interact with others as such.