Periculo: Your entire argument is based on perceived value.
So the question then becomes. Is the perceived value of the human race more important than the means by which the human race is preserved? My answer would be "No." As I hold no intrinsic value in a species, albeit unique, that I find largely antagonistic to it's biosphere.
But an unbiased answer should be: "Unknown".
However, this is not why I find the "Rape to save mankind." wrong. The answer is twofold.
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Firstly, the rape cannot be acceptable, because the value of the rape cannot be ascertained. It "can" be decided upon, but not without bias. Would "you" accept being raped to save the species (and for the exercise, it must be considered that the act is violating and unwelcome). I doubt you would be so reasonable as to truly say: "I do this, so that the human race may continue."
Who made the judgement on the value of mankind? If both parties believe the act necessary. Then rape cannot happen. If the rapist believes the act necessary, but the victim does not, who's value holds more credence? You cannot say which. But I will say that the rapist is in violation of another sapient beings choice (which is SO condemned in the Chantry).
What IS going to happen, is that one human being is going to utterly disregard the desire/need of another human being for a belief it cannot provide true value for (again, this is the Chantry in the aspects it is condemned for).
So it is with all crime.
If you steal bread to eat. You have placed value of your survival over another's need to make an honest day's wages (ultimately, their survival). There is no intrinsic value in one person's survival. The human race is a speck, on a speck, in a vast sea of eternity.
If you lie to save someone's feelings, you have placed your own agenda over the truth in order to manipulate a person's feelings under the presumption that you know better.
The ONLY morality is the ethic of reciprocity, otherwise known as the Golden Rule.
Does no Meredith believe she is saving the world? Or Alrik? If the majority agree that they are, then by your standards, the mages must all be tranquilized... and it is a "good" thing, or at least, certainly not evil.
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Secondly, the act of acceptance of such acts encourages such acts.
Sun Tzu knew this and warned against the danger of it when he said: "Those who celebrate victory are bloodthirsty, and the bloodthirsty cannot have their way with the world."
You cannot trust a man who celebrates and rationalizes killing to ever look FIRST to the option of peace. You must always worry that the bloodthirsty man will not only seek war, but also seek to undermine peace (we see this with Gaspard).
So it is with all other immoral acts.
You cannot trust a liar who excuses his lies, nor a thief who excuses his theft, nor a rapist who would excuse his actions as simply "being".
BUT, even if you are brought to lie, or steal, or kill, or rape... have the decency to welcome condemnation in its measure.
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Note: I couldn't care less, btw, of any spiritual implication of morality.