Etymology is certainly interesting, but is not relevant to current definitions of words. Words change their meanings. "Indoctrination" may well carry either positive or negative meanings depending on which people you talk to, which is why it's important to have discussions like this one. Many and many arguments have resulted because the two sides didn't agree on what their terms meant. The point is, we can decide that "indoctrination" refers to the act of picking lemons, so long as we're consistent about it.