Maybe I'm giving Bioware to much credit but I'm still thinking that the indoctrination is intentional. It's been a major theme in all 3 games and to me it's one of the reapers most powerful weapons. Here is a great video about the indoctrination theory. Won't imbed it due to spoilers, in case some have not finished or even played it yet.
*Spoilers*
http://www.youtube.com/watch?v=ythY_GkEBck