By preventing a larger, even more lethal conflict.
Remember, Itachi supposedly did what he did because he experience the "horrors of war" at a young age. To him, it was better to simply assassinate the Uchiha than to inflict the full-scale war their rebellion would have caused upon the village.
Again, I don't agree with that. It's more of that bullshit ninja world reasoning. I'm just saying that is Itachi's justification to himself.