Isn't that why, for example Eve and other MMOs, have invulnerable NPC bases where you could stash your things and zones friendly to new players where NPCs would punish people who try to PK ?
Most MMO's simply put everything that the player is and has completely outside of reach when they are not online. Classics like World of Warcraft have your character vanish when not being played, and all of your stuff either vanishes with you, or is in a extradimensional bank vault safely inside of a faction city that no one but that player can access. While the other side CAN attack a home city, they cannot actually destroy anything that doesn't immediately respawn.
Of the online games that do allow for total destruction, they generally
restart everyone from scratch on a new game. Something like Starcraft for example, win or lose, everybody starts off equal again at the beginning of the next game. Total destruction is okay, because no matter how much you build, you know its all going away at the end of the current game anyway, and then you'll all be handed a fresh start.
Eve is one of the very few games that combines the two, and yes, they have high sec(urity) space and low sec space, and even no sec. The player is then allowed to make the decision if they want to be mostly safe (but where resources are low), or take risks and push further out to better resource zones in less controlled space.
In Starmade terms, it would be like having the Trading Guild automatically go to war with anyone that attacks anyone else in their sectors, but who have ships big enough to absolutely roflstomp virtually anybody dumb enough to try. Those high sec raids are generally suicide missions.
Right now, Starmade has nothing like that. The worst thing that can happen is that you can't visit a shop for a while if you piss off the trade guild, whoop de doo, all the time you are getting a steady stream of pitiful little ships trying to attack you that you can eat for blocks.
If we were to bring something akin to secured space into Starmade, it would basically just turn into the same thing we have now, except instead of everyone turtling in their own 1 man faction base, they'd be turtling in an invincible NPC base.
Biggest problem we have right now is that a single base can do everything. We're starting to change that a little bit with reactor chambers, but its not nearly enough. We need an incentive to be the carrot, to give a suitable reward that makes players want to take the risk of expanding. And yet, it has to be balanced against the idea that the game still has to be playable for those who don't want to take the risk.
High risk, high reward. Low risk, low reward. And I have to admit, I don't have a perfect answer for that beyond something like in the OP, some kind of resource or objective that cannot be achieved with a single base, but doesn't cripple your ability to build if you don't have it.