It seemed as though Extremis may also be responsible for personality shifts, especially promoting violent tendencies. Pepper was quite surprised at what she was capable of under the influence of Extremis. Just imagine what someone who was already conditioned and trained to use violence would be capable of - in fact, you don't have to imagine. The Extremis subjects demonstrated it. Why would they betray their ideals and assist in attacking the US? Maybe they already felt betrayed by it? Who knows what circumstances they were in prior to finding themselves under AIM's care.