What you're seeing on the reverse is unavoidable--the dreaded purl bump.
You have the right idea about knitting the scarf double, but it's much simpler to knit it in the round rather than seaming it. You could use a 16" circular needle and just knit and knit and knit--no purling, and all the bi-colored bumps are on the inside. All the strands from changing colors can hang in there, too.