Yes! Written in Stone is/was one of the missions I am currently playing, and this was the conclusion I came to as well. I think the story (what I have found of it) even supports this course of action. These are clearly not happy people. Killing them is a mercy.
However it seems I am just not good enough at combat to kill all the enemies with the resources I had collected to that point, so I ended up putting Written in Stone on the back burner in favor of other FMs. At some point I'll return to it and most likely finish it up using notarget. The world geometry itself is lovely and I want to take my time to admire it without having to worry about enemies.
In terms of trying to diagnose what made the balance between exploration, puzzle solving, and enemy presence not work for me in this mission I'd draw a comparison to Iris and Hazard Pay, which presented similar challenges for exploration and puzzles but did not make me want to genocide the entire map.
The first useful thing they did was prominently signpost important locations for the player, often with actual sign posts in the game world, and in Iris's case with markers on the map.
Secondly they provided lots of safe corridors (that were easy to find) for efficient traversal between key locations. These safe spaces also often included overlooks or vantage points with clear views of the hostile areas so they player can get an understanding of the layout and plan their next moves without time pressure.
And lastly in places where the player does not have the benefit of signage, maps, or prior visual scouting, these FMs revert to a much more linear level design. (Like a vine with side branches, instead of a spider's web or tree like labyrinth.)
Now that I think of it, a lot of my most favorite TDM FMs follow these rules: Requiem, William Steel In the North and Home Again, Volta 1 and 2... That's not to say I think being lost or needing to make your own safety (Rambo style) have no place in TDM. (Perversely, Down in the Bonehoard has become my favorite T:TDP mission, and it breaks almost all these rules at various points.) But in those cases where being lost or ultra-violent is the intent, I believe the change in playstyle should be supported by tailored story beats and a generous equipment loadout.