Yes, ActiveRecord is not a good pattern for large-scale apps. The reason it's in Rails is because it's very good for simple cases and prototypes. But there is absolutely nothing in Rails stopping you from adding a service layer in whatever shape you see fit, I'm a fan of interactors (https://github.com/collectiveidea/interactor), but use whatever you want, it's easy to plug in new directories into the app structure and get magic loading and spec running automatically.

I agree that Rails enables a lot of messes, but I don't think the solution is to make your framework prescriptive about every single detail. I'd rather have the flexibility and enforce some standards per project than expect the framework dictate everything, because once you hit scale you have to do your own thinking and architecture anyway.