Well, Shepard has shown to be a different class of person, I think. I wouldn't say he's immune to indoctrination, but cracking his will would be a difficult process even for someone like Harbringer. He's always been portrayed as someone who's rather special. I think the indoctrination theory is alright, but it definitely doesn't HAVE to happen.
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"When I was a young man, I had liberty, but I did not see it. I had time, but I did not know it."