User blog comment:Raven15Rq/Confusing Things in BioShock Infinite/@comment-4920092-20130412231509/@comment-1330314-20130414021318

Actually, the indoctrination comes later, in Comstock House. The Tower was made to isolate her and keep her powers in check until she was to be brainwashed. It was also supposed to keep her away from Booker, though that didn't work so well.