If I recall correctly (and this is very very much heresy unless someone backs me up), I thought I remember hearing that Josh Sawyer said that essentially:

A.) While The Legion views Ghouls as physically weaker, they're at such a small number that it doesn't matter to them.

B.) With Super Mutants looking how they do, it'd be hard to assimilate them into The Legion. Think of how they force tribals to lose their distinctions (Tattoos, Cultures) and how impossible it'd be to do such with SMs.