I've always loved this argument; so many sides, and I still don't know which one I'm on.
I think this is a great example of the 'alien' nature of some of the squadmates. While Garrus may look alien, he doesn't exactly act it--we routinely compare him to Batman, a human archtype. We argue his loyalty mission the same way we argue revenge in our own society--is it best to forgive? To avenge?
Thane, on the other hand, comes out with something that confuses and even irritates some people. He's an assassin who genuinly believes what he does is acceptable; he's just a tool, after all. People rise up, cry foul, argue whether he's been brainwashed by misguided hanar or if he's just repressing what he's done to feel better. There are some people I know who outright hate him for that belief.
This argument always makes me think of Legion's loyalty mission, and the choice at the end whether to rewrite or to destroy the heritics. You have two sides, arguing passionately about the evils of brainwashing, how it's better to die than to be rewritten, how you need the geth army against the Reapers and it's the lesser of two evils. But listening to Legion's dialogue, you realize it isn't the same as brainwashing in humans. It is literally rewriting their code--morality isn't a part of it. In Legion's own words, "No two species are identical. All must be judged on their own merits. Treating every species like one's own is racist. Even benign anthromorphism"
We react to Thane's beliefs in a human sense--it's what we know and understand. But we have to consider that to him, possibly to the drell, there is nothing wrong with it. We can't judge 'right and 'wrong', as we only have our own moral code to go off of.
In summary: Garrus' mission is close enough to our moral code for us to understand, to make judgements. Legion and Thane work on another level, one where we don't understand enough of their culture to properly judge, especially based off of human ideals.
[I still haven't made up my mind on a human level how I feel, though I guess that would happen]