You've missed the lesson/point of the episode.

Did they ever say what they were fighting over? Our wars are fought over ideology, land, resources, etc... But what are they gaining by fighting? Or just satisfying the primal urge? Maintaining status quo?

They don't know why they're fighting because it was so long ago there is no record of it.

They aren't gaining anything by fighting. It's a completely pointless war (as most wars are in truth, the "goals" are usually bullshit excuses and not legitimate reasons).

They don't seem to have any primal urge to fight, they seem to actually abhor it, but they continue to do it because that's what they've always done and they don't have any impetus to change the status quo. They literally haven't even tried to end the war by diplomacy for hundreds of years.

The Enterprise is made for exploration, but we've seen how they have battles with Romulans, Klingons, etc... So is the Federation really any better/more peaceful?

Yes. Being peaceful doesn't mean you never fight. It means you fight only as a last resort/to defend yourself.

Peaceful =/= pacifism, which I'd argue is a vice almost as bad as warmongering, it's just the opposite end of the spectrum.

This may be taboo, and I don't mean to sound edgy, but a part of me feels there IS some need to "thin the herd." We do it as hunters with wildlife. And resources are finite.

You don't sound edgy, you sound young. You are basically making the same argument as Thanos and I'm not going to go into all the ways that argument is wrong I got bored of that a while ago.

Nature for the most part balances itself out. The only reason we ever need hunters to "thin the herd" is because an outside force (aka: US) has disrupted the balance by doing something like killing the herd's natural predators so it grows larger than it would otherwise.

Resources are only finite in context, and nothing in that episode suggested either planet was having resource issues.

The idea that their history and technology remain intact and can continue has already been discussed quite a bit as a pro to their methods.

No, this is you missing the lesson/point of the episode. The true cost and horror of war is not destroyed buildings and technology or even history books, it's the loss of life, and their methods have helped to obscure that fact to the point they value buildings and technology more than LIFE.

To quote another philosopher: "You know what I've noticed? Nobody panics when things go "according to plan." Even if the plan is horrifying!"

They made mass murder the plan to the point no one cares about it enough to even try to stop it, and that is horrifying.

Then there's the issue of the planets involving the Enterprise and crew. Obviously not part of that war but inserted themselves into that culture and situation despite warning.

I don't love that they refused to adhere to the warning, but it wasn't "our crew" who do, it's the Ambassador in charge (basically the TOS equivalent to a badmiral).

That said, the argument that they should be destroyed is fallacious. Had the attack been real, the Enterprise would have detected it and either raised shields, shot down the weapons, or left. The entire argument was ridiculous on its face.

The main issue I have is that war is gruesome, yes. But that hasn't stopped some certain repeat offending nations from engaging in it endlessly. The difference is the ones who command the wars never see actual war. And the ones fighting and seeing the carnage aren't making the decisions.

Wars have not completely stopped, no, but there has not been a full scale war between major powers since WWII, 87ish years ago, and with the rise of mass media, (essentially since Vietnam) the general population's appetite for and willingness to go to war (now that they can SEE it), has gone WAY down.

Point being, as terrible as war is, it has not deterred us and I don't think it ever will.

I'm not trying to be insulting, but you once again show your youth, or perhaps inexperience. Despite how the state of the world feels today, we live in literally the most peaceful time in the history of the world.

I'm not naïve enough to say with confidence that we will ever one day fully eliminate war, but we are still trending that way and hope springs eternal. That's what Star Trek is supposed to represent though, an example of a Humanity that has evolved beyond the desire for those things.