I don't know it made sense to me. Healing Pepper and removing his shrapnel was because he solved the part of the Extremis formula that was backfiring. How is that not clear, they even took him captive to figure that part out. Because it regenerates he basically used it to keep himself alive while they removed the shrapnel which would have otherwise killed him.
Does not seem like a cheat to me since the reactor he developed in IM2 pretty much "cured" him from having to worry about being poisoned so this was just freeing him completely of the threat he already removed in IM2