While doing the tonal puzzle, if I let my follower too close, she attacks the dwermer centurion, which is still in the cage and can't be killed and I can't call her off. If I tell her to wait out of the way then something releases the centurion and it stops around. I can't kill it and and Jenessa won't respond to me. How do I do this and get out?

If you mess up on the puzzle then that is what happens. You have to solve the puzzle(s)

Reload a prior Save and remember to make a Save before getting too close to the Centurion. Katriah also can get into the "Kill Centurion Mode" and talking to Her immediately after grabbing the Aetherium Shard may be the only way to get past this area.

A Follower can be asked to wait before getting too close to the area.

I had to reload twice because the Centurion always became active even if I solved the Tonal Puzzle.

Worst case scenario, use an AOE Flame or Shock Spell to kill the Centurion.

Huh. That explains why it was invincible for me too. Only it was Sphere Centurion Masterpiece from Immersive Creatures mod, so i thought it was a mod bug. Even "kill" command didn't effect it, i had to "disable" it.

Never assume a bugged mod when the bug can be in the base game