There are plenty of ways to counter Storm. If Emma turns to diamond her organs won't freeze. Magik can just teleport to Limbo and take out everyone from the safety of another dimension. Or she could teleport Storm's head off or send her into the sun at bullet-time level speeds. Any heat-generating character might also be able to counter storm freezing them.
Karma's possession has always been defined as 'psyonic' and distinct from telepathy. Any telepathy she has is rather pathetic in comparison both to her main ability and to other telepaths. Her possessing Magik was used in lieu of Xavier's telepathy when the latter wouldn't work at all - not because she had better telepathy, but because it was not the same as telepathy. The way her power has been used makes it so that it is not evidence of any sort of vulnerability to telepathy of the sort used by Xavier, Jean, Emma, ect.
While this is just a theory - it is my belief that Magik has learned to turn her psy-shields off so that her teammates will trust her more and that she can turn them on again as need-be. Her immunity in the old days was usually defined as people like Xavier and Emma not being able to read her mind, with psychic attacks being largely unaddressed. Oddly enough her only feats for withstanding direct telepathic attacks as opposed to simple mind reading are from recent years, not from the era where her psy-shields were a recurring plot point.