Wasn't that mystic script that appears after a pod is used evidence of magic? That and this "MP" thing that appears on the loading screen— if that's false, then that's fine. Even still, 2B can one shot even with a pod blast, in addition to the laser beams that can bounce off of things in an unpredictable manner, along with bombs, missiles... Sure, Aigis can switch persona on the fly, but is there a persona that reflects gun or pierce or something? If not, because these attacks aren't physical, I don't see how the blasts would be cancelled out.
But, yeah, Aigis has no reason to not use Mudo or Hama, and we can't rule it out, since we don't know what she leads with. Saying "how do you know she'll lead with it" doesn't mean much, if anything it only says that her victory via that method is one of the possibilities of the fight.