Wikipedia says it in the first paragraph: "(Indoctrination) is often distinguished from education by the fact that the indoctrinated person is expected not to question or critically examine the doctrine they have learned."
Zed is specifically referring to this usage. You should never assume you are doing the Right Thing in programming, because you probably aren't, at best you're doing the "least wrong" thing for your situation.
I still hold that education (insofar as it includes reading and writing) no matter how you cut it is a form of indoctrination. I understand the common sentiment behind the ideal difference and Zed's words, but I also think that no matter what you learn you are expected to a certain degree not to be critical since by default (when learning something new) you usually don't have the slightest idea what to even be critical about at that point. I just think the notion that there is a demarcation between the two is not true.So using your own programming analogy, I think the goal of education should be to strive for "less bad" of an indoctrination.