That God would both prohibit and command violence appears to be incongruous. The problem is not with God, but with man’s understanding of His nature and intentions.You are welcome.
Ah... yes! God ordered the Israelites to go to war. And the Bible says (or at least heavily implies) that God places the leaders of the various nations over us. So when our leaders order us to war are we to understand that God by proxy is ordering us? I assume so, and here is where I have difficulty: If I were a ruler and wanted to solidify my power, I would codify my legitimacy into the religion of the people. I would make it religious canon that God ordained me and I would make it a sin against God to disobey me. Now, I'm not saying that is what the ancient Israelites did, but it seems quite a coincidence...
I think that the explanation of God’s command to Israel to go to war is that His original intent was to drive out the inhabitants Himself, but God turned the responsibility over to the nation and withdrew Himself after Israel sinned. In other words, His command to go to war was a consequence of their turning from Him.
While you are correct about Israelites, don't forget that they disobeyed God more than they obeyed Him.
And now you have just opened Pandoras box of the Muslim religion.........."Jihad"!