The Endless are already long dead, and the fuel to sustain these programs, these projections is the energy of souls, they've all but spent their own from their dying world and now look to ours to sustain their own. Its them or us. There wasn't another way, there wasn't, and never was, a hidden option of a feel good everybody's happy swish and flick of a magic wand to make everything ok tee hee, happily ever after.
We did what we had to do in order to thwart that plan.
Was it moral? Was it ethical? do we have to be ok with it? Well there's no universal yes or no to any of those. That's fine.