Yes they are indoctrinated, but so are the adults. The adults themselves are still indoctrinated from their childhood. The children have been raised as a muslim and you do not have the right to tell them that they are wrong. The answer is not to rip children from their families and force another or no religion onto them but to increase education until they can make that decision for themselves.
That goes for every believer of every religion. You dont have the right to take children from their parents and try to convert them to another religion.
I dont think there is a problem with the children being put in another Muslim home. I dont see a reason we need to change the children's religious beliefs.