Lets start by establishing that there are two types of indoctrination.
The first I will discuss has to do with extreme cult like indoctrination, such as Westboro Baptist Church (onto the children), and with my friend Angie (the anti theist) escaped from (did you know one of the Phelp's sons escaped from the cult too?).
This type is dangerous because it also socially separates the children from others as they are growing up. I would assume the children were home schooled and kept away from others, which would be very damaging to their social growth and ability to make friends in the future, not to mention limited to no access to different view points, ways of thinking, different looking, acting, or behaving people, other religions, etc.
There actually is a movement of those that escaped this, this cult mentality is often referred to, as the quiverfull movement, and the website dedicated to it is no longer quivering.
The quiverfull movement tends to reference the women involved, as the quiverfull is a reference to a bible reference telling women to have many children, the more you have the better, often used by the extremists to find, not only abortion, but contraception, even natural family planning methods, completely immoral and evil, however there is much much more in the quiverfull movement, and many types of people that escape it, and many different stories about what the worst part was.
The most common complaint was leaving it would leave them completely alone, family disowning them, no friends, no community. This is the most dangerous part of the indoctrination in the cultist extreme view. For us, the atheists, it has little social impact, because even the moderates do not take this type seriously, they have little, if ANY political pull or support. No one, outside of these groups, supports them, at all. Which is what makes LEAVING them so hard. Even the people involved likely do not take these seriously, but are too scared to openly show it. They may sneak off to have abortions or obtain contraception, they may buy their own bread, etc, but do not let others see them being "hypocritical", its all about how the society sees them.
The second form of indoctrination, is with the more moderate religious views. This does not make this type of indoctrination any better. In fact, this is the MOST common form of indoctrination, and is much more socially acceptable form.
This type has to do with taking children to church, exposing them to concepts such as sacrifice, death, Hell, forgiveness, and fear, but making it into something that seems nice, and happy, and truthful, and telling them all good people think the same way, directly, or indirectly.
This type, rather than relying on controlling the social abilities of the children, relies on guilting them, scaring them, teaching them from a young age to accept these things as fact, unquestionable fact.
I am most familiar with this second form, I grew up, and still live in, the bible belt, and was raised with the "Jesus died for you, but you deserve to burn in Hell for your sins" view.
The more moderate view retains more well meaning and otherwise intelligent and logically thinking people, and can actually mentally traumatize them far more, however neither type of indoctrination is acceptable, beneficial, or non harmful to the children.
Religion is a topic that I believe should be purely personal choice, and I believe teaching children religion to children should not be legal, if the religion has material that in another context would be illegal to expose children to.
For example, the bible has passages about child sacrifice (Judges 11:34 and surrounding passages) pornographic materials (Ezekiel 23:20), incest (Genesis 19:30), and many more that we teach children in CHILDREN'S church, or youth programs.
If these passages were from any other book, we would ban access to it, and teach those that try to teach it to CHILDREN as fact, with child abuse.
It is nothing short of mental and psychological abuse.
And honestly, would you want to show how true your religion is, by saying it can't live on unless you put children too young to think about it logically, or at all, into believing it is something to never be questioned?
So while indoctrination has a negative, abusive, effect on the children, at least it has the benefit of showing others that the religions that rely on it cannot possibly be true.