I'm not sure why you think this is a defence. The Council is absolutely a racist oligarchy enforced by the Asari, Turians and Salarians. How that makes an equally but separately racist motivation somehow... not bad (?) escapes me.
It's at worst morally neutral if you intend for humanity to dominate the other species as the Council already does, and if you intended to use the human advantage to institute a more pluralistic and accountable form of government (even if you give humans an inbuilt advantage like veto power or disproportionately large representation), it is actually better. I don't see anything inherently wrong with using political violence as a means to an end against a repressive system, especially if there is a high chance that destroying the old system and removing the old racist tyrants from power is the only way forward (and given that the Council has been in power for more than two millenia, that is a reasonable conclusion). As it isn't actually making things worse, I can't see it as a bad thing just because it isn't the Nirvana solution, especially considering the ultimate consequences are exactly the same as the neutral option. At least the Renegade option expresses the intent to deliberately try to remove the Council (the only way to do so), rather than the neutral which hides behind a tactical assessment (a flawed one at that considering more people die for the same ultimate result).
I take far more umbrage with the Paragon option. It gives its tacit approval of the extremely racist system already in place, but it is ultimately splitting hairs. Both options are certainly racist, no doubt. I see no need to single out one or another.
But that's what makes the choice dumb. I'd say it's incredibly stupid that the game simply forces you to choose between 1) letting her go and 2) not letting her go. She's clearly trapped there. No means to escape. Just calling for back-up and then waiting her out is super simple. You've got a whole spaceship! Just get another squad, BOOM problem solved.
It has nothing to do with optimism. Exterminating the rachni is dumb, when there's a tremendous benefit toward studying it.
So then why criticize only the Renegade decision but not the Paragon one? It is the far less stupidly risky of the two given the rachni history of inexplicable, genocidal violence.
Apparently it wasn't an option with the whole "race against time" nonsense. Why you are allowed to dither around driving the Mako on countless identical planets and slaughtering a billion irrelevant mercs in prefabs while the Reapers and Geth get closer to enacting their planned organic genocide is the better question, but there it is. No point in criticizing the Renegade for making do with what they have.
What benefit? The rachni aren't a galactic threat anymore, so there is no need to find weaknesses unless you plan on deliberately unleashing them again. Do you intend to use them as a weapon? In addition to the ethical problems with that, look how well it worked for Binary Helix. Do you have some moral imperative towards "diversity" (a galaxy where the rachni succeed in their previous goal of wiping out all other advanced species this time wouldn't be very diverse, but whatever). Why do you need to study her for that?
Both decisions are non optimal IMO (I'd have prefered to keep her locked up until someone more qualified could decide whether the rachni are still a threat and what to do with them), but of the two the Renegade one is actually more sensible with the information you have, Wrex's hypocritical shitbird reasoning and Shep's comically unnecessary sadism ("STAY DEAD THIS TIME") aside. We're talking the life of a single sentient vs potentially billions.
It's "15" people in the same way that Skyrim's 10 house not-even-IRL-villages are "towns". It's a scale thing. But quite apart from that, if they are infected with some weird alien mind control parasite, again, keeping them alive to study them is way, way more valuable them killing them dead.
As to why it's a massacre, we're back to point mind control.
And if we start not segregating gameplay, then the entire series is stupid. No game will turn on a 3-person fire team just going around fighting offensively superior numbers.
I was under the impression that the small outpost we dock at was just that (think Fai Dan explains it), and that the majority of the colony's population lives around the ExoGeni headquarters. Whether the 15 colonists are supposed to represent 300 (the total population of the entire colony according to Feros description) is ultimately still not very relevant considering the importance of the mission and the billions of lives that depend upon its success. This would also add another point to the argument for simply killing them, being that you can't reasonably be expected to incapacitate and restrain 100 colonists per squad member within a reasonable timeframe.
What value is to be gained, and who says we can't study them if they're dead? We're going to kill the violent mind controlling space magic plant monster anyway, so even if they survive whatever links them to it will be severed. Plenty of information can usually still be gleaned from autopsies, provided they happen within a reasonable timeframe after death.
Massacres generally involve killing people who can't or won't fight back. The colonists are very much shooting at and attempting to kill us. That's called self defense. It's ultimately not much different than gunning down a Reaper husk.
The gameplay has an explanation for that, though. Space Jesus and his disciples are frequently described as inhumanly competent (or everyone else is inhumanly incompetent). It's a stupid one, but it is provided, as Shep and other squad characters make reference to literally killing thousands of enemies as the player does in game. That the game is illogical by realistic standards of infantry tactics (where you don't have plot armored ubermensch) is not an example of a failure of gameplay/narrative seperation. By contrast taking out the colonists with non fatal means is supposed to or implied to be more difficult or time consuming according to dialogue, yet in Min/Max terms it isn't.
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I have to admit being evil with your enemies is quite enjoyable I was never a full Paragon nor Renegade.....I just wanted to be nice with my squadmates and ruthless with my enemies. Paragade perhaps? Sure I don't mind being a jerk it's quite fun.
. Every next playthrough I picked only red, that wasnt even in question. I simply couldn't resist — it was so well implemented!! The difference from the blue option was often so drastic and so much more rewarding and satisfying, it wasn't just a paraphrase of the paragon option — twas a completely different course of action with follow-up reactions. That feature of the game was awesome. I really missed being a rude ass violent mofo in me3 and in da:i. Now that I think about it that was the only thing that made me keep replaying ME2 over and over again just cos I couldn't get enough. I can't think of any game that offers an option of being a badass "couldnt-care-less" protagonist without making them seem like bloodthirsty maniacs and at the same time making the experience so awesome. 
