Yes, I think you've hit it on the head there. Upping the stakes means that the peripheral characters (your favourite Chemistry teacher, a friendly town doctor) gets injured/killed.The stakes in "Stranger Things" were pretty high, and I'm not sure that would suit the Loop setting, but OTOH, without a sense of real danger, it will just be kids playing in the woods. One way of upping the stakes is to have bad things happen to NPCs (classmates, friends, siblings), or introducing potentially lethal situations (getting lost in an underground maze, stalking/avoiding sentry robots and dinosaurs, and so on). Having something happen as outlined in the post above sounds like a great idea.
"Tales From The Loop" isn't a game about a group of kids dying trying to uncover Mysteries. It's about how solving/not solving a Mystery will affect the world. The characters might not die but the repercussions might be dire for the community you live in.