With the way development is going, it's no longer going to be just a survival, it's going to be more focused on the world creation and interacting with other players/factions, similar to EVE, which is why it's valid to use examples from EVE to implement these sort of features. And I'm not suggesting war-game either, again, this is simply for the sake of opening up war, which has been one of the most prominent things in Starmade history. In a living world, there will always be war, and with invulnerability, then a faction can store all of it's ships at a mega shipyard, thus negating the war entirely, they'll lose a few stations, but keep everything else. With invulnerability gone, then it'll remove the reason to store everything at one base and never lose it, thus allowing war to actually happen.
This system may not seem perfect to you, but this is the best I can come up with, and so far, nobodies proposed any better systems, only saying no because they want invulnerability, or that it already exists. If there are any better systems to do this, then for the love of god, put them here so we can improve it, and make it a system that everyone can agree on. I'd rather not have to deal with "How about no?" and having to repeat myself.
How about, when a new player joins a server, they get 24 hours of active time protection. So, after 24 hours of them being online (It can be over whatever time period, doesn't have to be consecutive), then they can be attacked, but until then, they are immortal to all other players. I actually quite like that. :p