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This is pretty much The Other World's Books Depend on the Bean Counter, where the protagonist is an overworked office worker who accidentally gets summoned to another world. He has no special powers, and actually gets sick from magic because his body isn’t immune to it. The treatment for this is somehow gay sex with his aristocrat lover, which as far as I know is one of the first just straight up gay sex scenes in anime shown on screen. Overtime he accrues political power by basically single handedly auditing the country’s treasury.

They're eventually accused of being an agent of satan for having knowledge of things they could not know otherwise, and are stoned to death

This is a misconception, in reality the drinking water is about as safe for you as the cider. Both are riskier than most first worlders are comfortable with

Wouldn't boiling my water make it safe as well?

From Londoner to Lord on Royalroad takes a long time to get there, like it takes a long time to get anywhere, but recent chapters have been about a raid to free slaves. One of the first things the protagonist does upon becoming lord of the poorest village in the land is abolish slavery in his own holdings, and builds from there over time to sending out covert agents and raiding parties to free slaves and kill slavers. Other things he's done include building social housing, starting food and literacy as well as medical research programs, arming women, and land reform.

The minute to minute story is much more about long conversations about how to build things like seed drills, water wheels, and crossbows, though.

In one of the early arcs of Mushoku Tensei the moral compass character repeatedly massacres slavers and it's unambiguously correct even from the vapid, amoral shitbag protagonist's perspective. It completely drops that later on as the protagonist literally has no values or beliefs and just wants to be some guy with a quiet life who doesn't do stuff, which is the biggest failing of the later arcs of the LN series.

May I Ask For One Final Thing is technically an isekai, but the protagonist is a local of the world and the first arc revolves around her beating the living snot out of aristocratic slavers.

Roll Over and Die is one of those fucking things instead of an isekai, but opens with the protagonist being sold into slavery and is notably quite negative on the whole institution and the systems that interact with it.

It takes The Wandering Inn 10 volumes but eventually the main protagonist kills a bunch of slavers who try to enslave her after another side protagonist gets enslaved & escapes. The institutionalized slavery country though, whose politics is literally "Yay slavery!" still exists afaik and the last I read they were allying themselves with the terribly fucking written "I got transported to another world so I've decided to bring the gospel of American Christianity to the people" character against the "Yay necromancy communist utopia" country but I'm like 20-30 chapters behind probably so who knows at this point.

You've gotta read 8 volumes worth of "Yes, the world at large - well mostly...actually it isn't really 'mostly' but still...hates the slavery country and bans the slave trade" and various mentions of "the slave country should be destroyed" but nothing ever gets done about it plot wise until the slave country literally enslaves one of the main PoV characters and even then...he doesn't destroy the slave country because he has PTSD from being tortured as a slave but swears he's gonna come back to do so - which honestly, is probably how volume 10 will end if I had to guess (assuming it hasn't already...like I said, I stopped reading when the [Prophet] character got a bunch of chapters about how he's walking across the desert continent (home of the slave & necromancy countries) and has decided to destroy the necromancy country because 'unholy' despite the slavery country being right there...ok bro)

There's the John Brown one, but I dunno if that counts.

Related: one of my most cherished moments from Fallout 2 was being able to come back to The Den late in the game and liquefy the entire slaver's guild with a Bozar.

I know Beam already mentioned it but John Brown a stand in for the Shield Hero guy in the first chapter.

reincarnated as a toilet in another world

When I went to Vietnam, I got traveler's diarrhea from eating foods that locals ate without issue. There's a reason it's called traveler's diarrhea. It turns out that when you go to a place with bacteria that your body isn't used to, you react worse than people who've had a lifetime to acclimate to them.

locals can be used to something that won't kill or impede you much if you're used to it and breastfed from someone who was used to it that will ruin the regularity of someone who does not have compatible gut fauna.

I would find such scenes less offensive than slavery apologia