Use Amon, the regular one you get from the story. She has a skill that can be pre-activated that give a 1 time permanent buff that will protect from any debuff/affliction once, then it needs to be reapplied.
Use Phoenix as a sub or friend support to help with affliction resist or Behemoth to remove affliction if you have it or a friend. If you have Mordred, she also has a increase affliction resist ability.
Be aware that Medusa uses it at random, sometimes she might not use her petrify and other times she might just spam it. You do not want to be petrified during her rage, she will use hard hitting single target attacks and kill off your party.