Exactly. It washes him of responsibility for his actions. He just becomes a victim, a puppet. It was really the Batarians who killed themselves by being dumb enough to test advanced hallucinogenics on armed hostiles who wanted to kill them. Shepard was nothing more than a temporary vessel for their stupidity and arrogance. He's not at fault, because he did not choose, of his own free will, to kill them in cold blood.
I'm actually glad that you mentioned the Batarian thing, because I was thinking along similar lines. Assuming that all of the origins and psych profiles happened and co-exist, Shepard's life could be summed up as "would have been a successful happy life, Batarians fucked everything up, kept fucking everything up, and ultimately got fucked up."
Shepard watched them kill, butcher, enslave, and drag off his entire nuclear family, his friends, his teachers, his neighbors, and the woman he loved and had asked to marry him. The only family he has left is his aunt, stationed on the Einstein, and Hackett, who is not actually related to him, but is an old friend of the family who helped Shepard pick himself up.
The Colonist has the justification for hatred, murderous hatred, of the Batarians. I like to think of Shepard as being a professional, but if that pirate base had a slave pen in it, if Shepard had seen that, what they did to their slaves, their female slaves in particular. . . I'm not sure he could not lose it.
I will say, though, that I want to keep the element of the Alliance screwing Shepard over during the trial. It's important that that's there, because Major Kyle becomes an established, recurring villain later (though not an unsympathetic one), and the fact that the Alliance brass favored him over Shepard becomes a plot point.
Maybe Kyle losing most of his men and Shepard's rampage were completely unrelated events that had nothing to do with each other (i.e. Shepard technically didn't break mission to do what he did, since the mission had already been stated to wipe out the base, and what he did had no effect on the outcome), but somebody had to take the fall for the mission losses? So instead of the slap on the wrist or stern frown that they might have given Shepard ordinarily, they decided to make him the scapegoat to try and save Kyle's career, and pinned the entire failure on him, blaming him for the loss of men and not glossing over the casualties of what were technically non-combatants (because they had surrendered), which they would have done normally, because it's not like they like slavery, pirates, or Batarians either.
Which would have lead to Shepard's dishonorable discharge from service, but Hackett and a few other members of high-ranking Alliance brass put their foot down and refused to drum Shepard out for something that they normally wouldn't have cared about over dirty politics.
Which leads to him being stationed on Akuze in a dead-end position guarding the intergalactic version of a snowman, which leads us directly into the Survivor part of the psych profile (CERBERUUUUUUSSS), which I fully intend to exaggerate into the realm of "no human could have possibly survived that," only they know Shepard did, because they have the recordings in his helmet to prove it (remember, Shepard has a powerful, passive connection to the Force. People with such connections can stave off necessities like having to breathe, eat, or drink for hours, years, and months respectively). Remember, the fact that he survived Akuze at all is supposed to be a big deal. While that makes sense if that's the 'only' thing he's really done, it doesn't make sense for people to make a big deal about it if he also has a Star of Terra and the reputation as the Butcher of Torfan.
I'm compensating for this by making it so that Shepard was forced to endure conditions that would have killed any human, for a period of time in which he should have definitely, absolutely, no questions asked, died of dehydration. He did this alone, out in the middle of a lunar wasteland of desert-like heat, arctic cold nights, and solar radiation, with no protections from the elements besides his failing suit and whatever rocks he could take shade behind. Shepard literally survived something that is medically and scientifically impossible for a human to survive, ever, even with extensive (illegal) genetic modifications. We, of course, know that it was his connection to the Force that saved him, but the galactic community doesn't, so for all intents and purposes, Shepard is the guy who had a submarine implode on him at the bottom of the ocean and then walked it off. It is, literally, a goddamn miracle. No one can explain it. Salarian and Asari xenobiologists and various human professors of medicine have written thesis and published papers about this. It's not a secret. People outside the Alliance know about this. It made galactic news. They examined him extensively to try and figure out how he could have possibly survived (which, naturally, turned up nothing). It's a legend in the Alliance, almost memetic, like the stories modern soldiers tell about those mythical maybe-true-maybe-not badasses who "totally for real" used an aircraft machine gun taken off of a downed bird to saw incoming enemy combatants in half.
Only this is no bullshit, because this story has a name, a medical record, published papers, and a face. Commander John Shepard, "that guy who just can't die."
Which leads to Shepard being forced to take paid leave by Hackett because he needs to recover physically and psychologically ("You need a vacation, Shepard. Don't make me tie you to a chair and ship you out of here in a crate."). So he goes on an extended vacation at the popular resort world of Elysium. Cue the Skyllian Blitz. Standard defenses crumble, Shepard rallies together a group of on-leave soldiers and civilians, not all of which are Alliance, or even human, and pushes the attack back, leading from the front. The pirates and slavers, not expecting this kind of resistance, get steamrolled and pushed back to orbit and the forest fringes. Shepard then holds the entire resort-city for the half a day it takes for the Alliance Navy to arrive. The SSV Agincourt (which Pressley happens to be on board at the time) knocks so many carriers and fighters out of the sky the Pressley lost count, while coordinated fire from the ground under Shepard's direction kept the slaver transports grounded, allowing for every single person taken by the pirates to be rescued.
Number of civilian losses: 320
Number of militia KIAs: 5
Number of slaves taken: 0
Out of a resort population over 3 million strong, only 325 people died, the vast majority of which were killed in the initial assault. Out of the entire joint militia of on-leave soldiers (Alliance, Turian, Asari, and Salarian), only five suffered KIAs, a feat credited fully to Commander Shepard's tactical skill and leadership ability.
The pirate and slaver coalition suffered a crushing defeat, and was forced to withdraw to prevent total destruction. Elanos Haliat, the leader of the initiative, was ruined, his credibility in the Terminus Systems shot. He swears vengeance at any cost on Commander Shepard, and becomes another recurring villain.
Shepard is hailed as a hero across every news station and program in Citadel space. Hailed for uncommon valor above and beyond any calling, he receives honorary medals from all three extrahuman militaries for his actions in service of a higher cause. The Alliance awards him the Star of Terra, the highest possible honor it can bestow. It has only been given twice before, and both times it was awarded posthumously, making Commander Shepard the first living person to receive the award. The event was covered live. The story, and various accounts of the Blitz and the actions on ground, aired almost nonstop for an entire year. Books were written about it, including several 'inspired by real events' fiction novels, and no less than five video games were made relating to the event.
His skills unquestionable, and his integrity almost beyond reproach at this point, Shepard is recommended for elite special operatives training by Admiral Hackett, and is fast-tracked into the N7 program. He attains full N7 status in an incredible amount of time, breaking all previous records, and in accordance with the N7 requirement of practical field-usable higher learning, he attains a doctorate in Engineering at Grissom Academy.
He had a distinguished career as an elite N7 agent that spanned over a year and a half of service. It was then that the he was pulled from standard spec op rotations to go on an unexplained test flight of a cutting edge vessel that featured untested stealth technology.
And so it begins.
What do you think of that?