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Mistborn Era 2/Stormlight spoilers
Just gonna go out on a limb here, but I think the big bad organization Wax’s uncle is working with is preparing for some sort of Cosmic war thing. The things they are doing are utterly reprehensible and the only way I can fathom them doing it with a good conscience is believing it’s for the “greater good”. So with the knowledge that the government is… well, made of these men, and Harmony isn’t corrupt, the only thing big enough to make this make sense (obviously to a demented, immoral mind) would be an out-of-world threat like Odium or another Shard.
I imagine their justification is something like “You see what you did to that building, Wax? With these children we can selectively breed allomancers and feruchemists of whichever type we want, then combine their powers with Hemalurgy to create impossibly powerful soldiers. Imagine an army of 100 Miles Hundredlives! We’d be unstoppable.” With knowledge of hemalurgy and compounding and all that, I imagine they’d independently arrive at the concept of making another Lord Ruler, which like… would be extremely difficult to deal with for anyone we’ve seen in the Cosmere. But yeah, they’d feel they were doing the right thing, “making the hard choice for the greater good”
Then Wax would be all like “but the cost in lives is ridiculous! This is not worth it, man, can’t you see that?” Blahblahblah blah. This is a stretch, so I’d not be surprised if it’s something totally unrelated, but a lot of Rhythm of War is spent ranting about an impending God War, so it doesn’t seem unreasonable.