The "Shepard is indoctrinated" theory is so, so stupid. It's just people trying to make those horrible endings easier to swallow.
The forum post on BSN explaining the new reapers' goal (was that written pre-leak?) is spoken so much better than what the Catalyst says in the game. It's better than "DAAARK ENERGY!" for sure, because it actually characterizes the reapers so infinitely better than what we received in game.'
Fanfic time?
First of all, it should have been a discussion with Harbinger. Maybe the catalyst should have been harbinger, or some energy core that's in the center of his ship. It should have been inside the Harbinger ship, and he should have been hostile and had a stance more akin to "how can you not appreciate the work we've done to preserve organic life in the galaxy?" But you begin to understand both their perspective and why it's wrong, and you can use your achievements at Overlord and with EDI and the Geth that even AI can reach peace with organic life to justify your decision to end the reapers. Maybe Harbinger can be persuaded by Shepard that what she's done is enough to prove that their summations are false and gives Shep the catalyst, or the renegade version is you unplug a bunch of tubes and Harbinger's core becomes loose so you acquire the catalyst in this fashion.
Best ending: Activate the catalyst from inside Harbinger ship, Crucible goes nuts, beams shoot out, reapers destroyed, Shepard lives
Good ending: All of the above, Shepard sacrifices herself
Worst ending: All of the above, but mass relays go with it, Shepard sacrificed
An example of the "Oh... now I understand the bad guys" that was done right is this one (the Matrix)
http://www.youtube.com/watch?v=rpKphB4w9ME Agents and reapers have similar roles in their respective stories.