The ending isn't indoctrination, it's just bad writing.
Bioware said so themselves in the Final Hours;
"On Deciding the End of the Game. The illusive man boss fight had been scrapped... but there was still much debate. 'One night walters scribbled down some thought on various ways the game could end with the line "Lots of speculation for Everyone!" at the bottom of the page.''
They pretty much ran out of ideas at the end of development.
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