In my game non-humans aren't ppl, therefore not children but spawn.
No, the end doesn't justify the means, never not IRL nor in my games.
Since an orphanage is full of the innocent blowing it up (by whatever means) would be evil (this extends even to your world where non-humans are ppl.
Let's use a different example, lets say that by exterminating all huwhite ppl the world would trully become paradise and everybody would join hands and sign kumbaya.
Does the end (paradise on earth) justify the means?
Now do it the other way around, do the means justify the end?
Lets say you were capable of harnesing the divine power and were able to eradicate all huwhite ppl by snapping your fingers (so no suffering or fear for them). You did it using God's power, does it make it Good?
IME when the players start doing those things you describe have happened in your game it's the fault of the GM for not making clear the rules of his world and not enforcing the alignment.
I don't think that I'm seeing you flip it the other way around. If destroying innocent lives is Evil, regardless of the method used, then saving innocent lives is Good, even if you use necromancy and curses. Just as shiny divine energy cannot redeem senseless slaughter, nor can gothic aesthetics condemn magic used to help and preserve others (with the proviso that the gothic magic can indeed have side effects that need to be considered).
I also think you're getting into some philosophical definitional questions, but I say it depends on your framework. In the standard of most games, there literally does not exist an authority that can say the future with any accuracy, since the future of game worlds relies on dice and player decisions, so I'd fight the hypothetical about ethnic cleansing being known to cause utopia, even before we look at how often that has historically worked. But absent the hypothetical-fighting, it comes down to your moral framework, of either doing the most good, or embracing rights absolutely. If you could preserve the lives of hundreds of trillions by killing billions, then you clearly should, just as we accept that we need to go to war to stop an aggressive enemy and accept that we will be killing a measure of that enemy's civilians, the truly innocent among them, as collateral of the violence we need to stop an aggressive nation from waging war against us.
But plenty of moral systems do not accept the idea of necessary sacrifice or the greater good, and condemn any such calculus. If you believe that killing the innocent is always wrong, and that, e.g., the bombing of a tank factory in WWII is unjustifiable because the people making the tanks for your enemy are not combatants (and would probably be jailed or shot for not supporting the regime controlling them), then you would condemn the bombing, even knowing that more soldiers (yours and theirs both) would die if the factory stood.
When I use D&D good-as-planar-force, I myself emphasize that Good and Evil are bits of physics. They're not sentient, they can't plan or look ahead, and it's all about what decision you make in the moment. In my campaigns, the forces of Good and Evil don't care how many lives you saved by killing an innocent crucial to the evil plans of the Dark Lord; what matters is that you killed an innocent.
But (also IMC), actually using the planar energies utterly swamps the residue left from deeds, unless the deeds are truly epic in scope. For most of the examples (clerics and aligned outsiders), you either need to keep a code of conduct or lack free will and aren't really capable of attempting to do Good with Evil and vice versa, but in the specific case of wizards who use aligned spells, they can pretty easily disconnect their actual alignment from how those around them tend to perceive them.
Now, D&D is also quite different than most moral settings in that D&D is explicitly mirrored. Good is the metaphysical opposite but balanced pole of Evil. What one can do, the other can do in reverse. In that model, you need to take into account that if bad ends corrupt good means, so therefore should good ends redeem bad means. In settings and moralities without that cosmic balance, you can say "No, bad ends or bad means make it bad, full-stop."
But when you just call specific magics evil (or, as you point out, good) without looking at what they actually do, and who they actually do it to, you end up disconnecting the actual essence of Good and Evil from what people tend to consider them.