but it seems that according to lesswrong doctrine, they are above the sanity waterline while my first friend group is below.

No. Having religous beliefs places an upper bound on how rational a person could be, past a certain level of rationality, a person will necessarily discard religion. But this does not mean that any particular atheist became an atheist by achieving that level of rationality. Most have not.

The article Raising the Sanity Waterline proposes not directly arguing against religion, but to instead teach the skills that would enable people to level up to the point where they systematically reject religion on their own, in part because just getting someone to reject religion does not actually make them more rational.