I think that's already quite off topic from the OP's question, but I'll risk further derailing the thread...
Both sides lose... well that's what war is
Co-operation
should yield more economic benefit than war, so in that sense things seem about right.
This is a video game, not a complex representation of actual conflict and the manifold consequences thereof.
Combat, in particular between players, is one of the primary pillars of the game, especially at the game's present stage of development. Throughout the game's development, PvP combat should, and most likely will be, improved and justified (through economic or other gains).
Cooperation should still produce relevant potential for economic gain, but in games, risk/reward should be given consideration too. It's fairly logical, in this context, that the greater risk of PvP combat should
probably offer greater potential reward.
Direct, short-term economic gain (aka. "loot") shouldn't be the reason for war, even "if it's just a game". It may be reason enough for a skirmish, but not for a war. It may be reason enough in a simple shoot-em-up game, but I hope we can agree that StarMade neither is, nor intends to be, just that.
What you expect to gain from a war are
indirect, long-term economic benefits, by expanding your territory, thereby gaining more resources, and/or denying same to your opponent. For that goal you have to expect to expend resources first, by going to war and sustaining damage, which you
hope you will make up for after you have won. If you can't at least hope to benefit in some way, don't go to war, period. If you risk starting a war by initiating a skirmish, maybe think twice.
If you want to just spar with no risk of loss, set up the conditions - a creative mode PvP server may be the thing.
In my opinion, on a survival server economy should be very much the fuel that drives everything, not the prize ships you capture from other players. That may be the icing of the cake, but you have to have the cake too, even if it sometimes tastes like saw dust.
Currently there are few reasons to expand territory, because almost any system already has everything, so why fight over the system that's between you and your neighbour? Uneven distribution of resources that don't respawn, or slow enough to drive players to explore and expand, is something that has been added only recently, and the upcoming addition of NPC factions that compete with players over those resources can be expected to create more competition, and thus more reasons for conflict as well as cooperation, both PvE and PvP.
TL;DR:
Even in games, a Pyrrhic victory should always be one of the inherent risks of a conflict, unless you're talking PacMan or Space Invaders.
And even there, you don't gain anything from the "war" - in the end you always lose everything, you just try to last longer than the ones before you ;)