Which standing stone is better for negating magic damage?

Atronach, IMHO, because it gives an average of 50% reduction and it refills your magicka. It's especially good if you're a Breton because it stacks with the racial power to give total immunity once a day.

That is what I figured but wasn't sure if it took 50% off of damage every time or absorbed all damage 50% of the time.

Yes, it absorbs all 50% of the time, maybe not obvious from the description.

I'm playing on Master so the fear of a one-shot is very real. I might stack The Lord Stone with the passive resist perks from Alteration. Glad I got that classification because I was definetly misreading that discription.

It's 75% if you are a vampire with necromage, if you combine this with the 30% from the absorb you get from the alteration perk, it pretty much breaks the game vs magic users and makes dragon fights a joke if you stay out of melee range. I don't recommend it at all.