> Indoctrination (noun) - the process of teaching a person or group to accept a set of beliefs uncritically.

I understand what you're saying about conflicting value systems, but you're flat-out wrong that what the author describes is indoctrination. The key word from the definition is "uncritically".

Here's the key part of what you've quoted:

> they learn to think for themselves, that they ask a lot of questions, that they question authority,

All that is the opposite of "accepting uncritically".