For one thing we don’t view life and death the way it was viewed in ancient times. There was an understanding that you carry the spiritual seed of your people and you are corrupted to the level of your society. The choices of the fathers are the experiences of the children and lead to a path for your people-choices become habits that become your culture. Every person within a society is corrupted by that society. This is true today but we don’t seem to have an awareness of it. I am a product of my society as a whole and my family specifically and I cannot be who I am not-I can only make the best choices that I can make based on where I stand. And my children were born at my level of righteousness and/or debauchery-and shot from our bow in the direction we are headed. So a child born into a pagan culture that hates God and sacrifices children in the fire and all sorts of horrible things that you can read about being done by the pagan communities in Biblical times 
was born into a spiritual level of evil that would be a lot to overcome. It would be one thing to redeem them from that, but it is another thing to try and save all the children and they grow up knowing all of the adults were put to death. It doesn’t really set anyone up for success to be “saved” in that scenario.
But with the belief that those who die move into the spiritual realm where they are able to attain levels of righteousness unhindered by the physical body . . . then children can be set free of the cultural trappings that would hold them back from righteousness. The children would be able to rise above the level of spiritual existence that they were born into-freed from it before they embraced it for their own.
And there were some communities that were just so evil that God said, Israelites or not, they were not going to be allowed to continue. The story of the Exodus involves God declaring that it was time to rid the evil people groups from Canaan. One belief is that Job had remained alive until that time and it was only after his death that God was willing to cleanse the Land. That, for Job’s sake, God had held back His hand.
So the Israelites, who had been promised the Land, are in slavery and crying out to God and the time is right-right Pharoah in place to accomplish everything, the Israelites ready to go in and take the Land (well, almost 
), the Land ready to be cleansed of the evil being done on it . . . and God tells them that HE will drive the people out ahead of them. And for the most part that is what happens!
Jericho was not a battle-it was a worship service. The events of the 7th day would have been on the Sabbath and did not involve “fighting” or blowing the call to arms, but the shofar is the call to worship. And when they all blew their shofars the walls fell down and everyone who wasn’t injured in the collapse of the wall ran off. The city was “utterly destroyed” which is also a way to say set apart for the Lord. Nothing found in the city was for the people-nothing was to be spoils of war. I believe that by the time they burned the city in Joshua 6:24, there were no people in the city. Of ourse that is just my personal belief-I wasn’t there to know for sure but neither was anyone else who might have a different opinion.
There were battles that the Israelites initiated-and they almost always lost them. God didn’t go into battle with them when they went off all half-cocked thinking they were great military victors 
There were some battles that were initiated by the other society and sometimes it was despite their best efforts to give the people space and go around them-and there were times that God told them to destroy everyone. And while I would never suggest that we should accept God doing evil to accomplish good (something I was reading someone argue for recently ) I will say that we cannot see the big picture and our limited perspective is truly that-limited.
For instance, Saul lost the throne for, among other things, not destroying all of the Amelekites. His choice to allow anyone to live led to the book of Esther. Haman was an Amelekite and Mordechai was a descendant of Saul.
I think it’s important to remember that within the stories there is a lot going on. There are some people who went off on their own, there are some people who did not behave in righteous ways, there are some people who blundered it, and there are some things that it’s okay to sit down at the end of the day and say, “I just don’t understand.” But when we condemn, we are saying we DO understand. When we pass judgment we are making very big statements about things we have limited perspective on. I don’t think a judgment that something we don’t understand is “evil” is any different than a judgment that it’s “righteous”. I think the humility to say, “That hurts my modern heart and sensibilities but I trust God and I have to believe there is a bigger picture I can’t see” is needed in very healthy doses with these things 
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