Heretic_Hanar wrote...
So, again, I have to ask: How does this translate to the indoctrination theory? For my Shepard there is no real reason NOT to pick the Destroy option in the end. Does that mean my Shepard is more resistant to indoctrination than any goody-two-shoes Paragon Shepard?
So does that mean that ruthlessness and cold calculus helps you to keep the Reapers out of your brain? 
Could be. Garrus: "The ruthless calculus of war - ten billion people here die so twenty billion people there can live"
But in this instance you're saying that you have your agenda, and you're sticking to it. You intend to pick Destroy, there's no reason for you not to pick Destroy so you're going to do it regardless of what the Catalyst tells you. So yes, you're resisting indoctrination. If you went into the final decision intended to pick Destroy, but ended up picking a different option after hearing the Catalyst's choices, then you'd be indoctrinated.
But imho, Paragon/Renegade doesn't really come into the final choice. The red/blue of the Destroy/Contorl endings is a trick, designed to confuse you and throw you off. Renegade or Paragon, Shepard advocates Destroying the Reapers with Anderson and Hackett. Renegade or Paragon, Shepard tries to convince TIM that Control is impossible. Renegade or Paragon, Shepard doesn't even contemplate Synthesis at all until the Catalyst suggests it.