Yes and it would also change your interactions with him, which is my point. If Saren weren't indoctrinated then Shepard et al wouldn't be taking issue with him for being indoctrinated, and you might actually have a (brief) discussion/refutation of his beliefs instead of his state of mind. This is all encapsulated by the fact that, as you brought up, when Saren realizes he's indoctrinated he kills himself. If he actually believed the Reapers could be reasoned with, that they were the next transcendental step for organics, that they would let subservient races be, then he'd go on trying to stop Shepard even after realizing they control him. Instead he realizes he believes these things because they forced him to.
I mean, changing the characters involved in any story would obviously change their interactions.
Ok, so imagine that you were Saren, and one day you discover about the Reapers, how insanely powerful they are and what they've done over the millions of years of their existence. Let's be real, you'd shit your pants, and I wouldn't believe you if you said to me that the option of negotiation never crossed your mind.
At that point, Saren chose to sort things out himself, because as he said, making this thing go public would mean the organic life would panic and go full on insane about it, ruining any chance he believed he had at resolving this peacefully. So he went to resolve this huge issue solo. With Benezia as his ''advisor''. And from there he started descending into madness.
Now Shepard reacted in a different way. He chose to stop them no matter the cost, and that was the only time you saw someone affect Saren so deeply. It drove him even more insane in Virmire where he let Saren implant him, even though he sort of knew that he was getting indoctrinated.
Both wanted to save the galaxy, in different ways. We don't know if the fight against the reapers is hopeless or not , what matters is that Shepard radiated his ideals through action ( of the narrative AND gameplay kind) , and his ideals caused Saren to choose suicide.
Also you gotta remember, sci fi is a powerful vessel for commentary for real life. The council was basically commentary on today's political system, and indoctrination was commentary on how people can be led astray to do bad shit.
This is also mirrored in the conversation path with TIM in ME3 where you get him to shoot himself. Shepard's response to TIM's position that the Crucible will let you control the Reapers and that this is better for humanity is "you're indoctrinated." Take the indoctrination angle away and it's a battle of beliefs again, like it seemed in ME2. That's why the version of TIM's death scene I'll always prefer is shooting him as opposed to letting him shoot himself, because his final words reinforce that they were two men trying to save the galaxy but having irreconcilable ways to go about it, as opposed to one dude being brainwashed and finally realizing it.
What exactly were the battle of beliefs in ME2? Almost nothing in that game made sense to warrant a serious discussion about beliefs.
Unless we're talking about the squadmate stories. I really really liked talking about Legion.
