actually omegas aren't disadvantaged in this world, it's flipped i believe. since they made mugo their god back then and could wish for anything they wanted, they wished for power and the "era of lunas" was like a violent overthrowing of the alpha reign that was in place already. also it was completely justified that they had to suffer and die, they continued the cycle of exploitation and abuse to the "branch family" just to keep their power. I BELIEVE that's the plot if not then i completely lost the plot (づ ̄ ³ ̄)づ
I would understand if all those deceased omegas are in the Kang family, because they got to where they were through dirty means; they claimed to use Mugo's power "for the greater good of all omegas", but ended up only reaping benefits for themselves. If that's the case, then I'd totally understand, though the authors really should explain more to clarify things.
But if some of the dead are other unrelated omegas, I'd be very upset. Seeing how omegas are still treated like pieces of tradable goods (e.g., sacrifice, surrogates, etc.) (aka slaves) & looked down upon (think the secretary's attitude towards the young family head), it just seems that even in modern day in this world setting, alphas are still the socially dominant ones & omegas are still under heavy discriminations. Killing off successful omegas when it's already much harder for them to make it is just... evil.
Did you even read?
Literally only the main Kang family omegas (that made the god) got powerfull over alphas and then they begin treating other omegas just like alphas were treating them before. So for majority of omegas nothing changed at all. And now they died and since the rest of society got civilized the rest of omegas got help.

That's not fair! Aren't omegas already the disadvantaged second sex in this world setting??