bns: I believe that the root word(s) and history/entymology of a word still have meaning. Indoctrination is one of those words that still carries both its positive and negative meanings today.
I believe that the negative connotation of "indoctrinate" and "indoctrination" became popular sometime early on during the Cold War and referred mainly to Socialism, as the OED cited. I can't find the exact point when it started being used that way, but it seems to be the very late 1940's or early 1950's.
I think the better terms to use are "propaganda" or "coercive persuasion". They're more accurate to the points trying to be conveyed and don't have conflicting usages, like "indoctrination" does....
We all have been indoctrinated but have we been propagandized? That's where our other thread comes into play
