Emma Frost did hold the title of White Queen in the villainous Hellfire Club before changing her ways and becoming more straight-up heroic, but only one X-Man has ever been worshipped as a literal goddess. That honour goes to Ororo Munroe, better known as Storm, better known as that character Halle Berry hates playing but makes a lot of money from.
Like the Hulk or Emma Frost, Storm has never had her weather-manipulating powers pushed to their limits, but it's possible they don't actually have any limits. Her control over the elements is based in a sort of telekinesis which lets her do...basically anything. Storms, thunder, lightning, rain, flash freezing of enemies, flying on the wind, making other people fly on the wind. She can control the temperature, even on other planets. Storm's powers even work on a micro level, as she's been shown to have control over the air in somebody's lungs and can herself separate the oxygen from water, this personal electrolysis allowing her to breath under the sea.
Besides all that Ororo has a will so strong that her mind is resistant to most psychic attacks, and her family history of witchcraft -passed down from her mother, herself the daughter of a powerful sorcerer in her native Kenya - has her down as one of the most powerful magic users in the Marvel Universe, rivalled only by Doctor Strange, and that's his whole shtick. That's a heck of a lot of power that Storm holds in her hands, so it's no surprise she's been identified as an Omega Level Mutant numerous times.