Indoctrination is teaching someone to accept doctrines uncritically, in other words, it is the end of discussion.
Many things we learn in school we are expected to accept uncritically: Like the numeric and alphabetic system, pretty much the whole of math, a lot of science. To say nothing of learning language, manners and basic skills like personal hygiene and cleaning the house.
Somewhere until the age of 12, children aren't even able to think abstractly, so to speak of them "thinking critically" is misplaced.
Education is simply an imparting of knowledge and skills, which fosters discussion and encourages critical thinking.
But the same is done in religious institutions, except it is done
on their terms.
A person won't just pass the church class by using whatever arguments they please. They have to use specific arguments to support their answers, they have to show some understanding of the doctrine.
Similar as in regular school.
The differences are centered around the willingness to accept without evaluation, in other words, to accept on faith; ie. religion.
It is not so simple, though. What you are saying above would apply only to "beginners" and those who aren't so "smart".
By believers, blindly regurgitating what one has learned in church class is not rarely regarded as inappropriate and disapproved of.
Moreover, there is more to this phenomenon you bring up: We have to take into consideration the
development of moral reasoning and the
development of faith.
According to the Kohlberg scala, most people fall into the Pre-conventional and the Conventional level of moral reasoning. Bluntly put: they cannot really "think for themselves". To accept things "on faith" and "without (much) evaluation" is the way to proceed for most people, religious or not.
The Fowler scala is somewhat speculative, but I find it nonetheless brings up an important differentiation between possible ways to have (religious) faith.
Most of your arguments against religion are justified only for religious reasoning in the first three stages of faith of the Fowler scala, but not for the latter three.
(Note that these latter three stages, or at least the last two would not even fit into "organized religion" anymore.)
Ah! Enculturation. Thanks.
I've seen both words used: "culturation" and "enculturation".