How do you reconcile this . . . .
To me, the whole idea of God cleansing the earth of the people who weren't loyal to him sounds like God condemning people that don't do what he tells them. You spent a lot of time saying they're different things, but I just don't see how.
If this is God's earth and his creation, then it is his property, much the same as a Landlord opens up his property for tenants to come in and enjoy living in his clean and well maintained residence. Instead of charging them rent though, he allows them to occupy his property on the condition that they act as the caretakers, maintaining things and keeping the property in good order. Those are the terms and conditions attached to the tenancy agreement.
Now suppose the Landlord on his return after a long absence, finds the property not only damaged and filthy, but the tenants have invited unsavory people to share that property knowing that they were not going to abide by the rules....? They allowed them to do damage and didn't evict them?
What options does the Landlord have? He can evict all the tenants there and then without giving them an opportunity to make things right, or he can allow the original occupants to clean up and repair the property and to tell their dodgy visitors to leave, whereupon he will come back after a reasonable time and make an inspection to see if his rules have been complied with. Which would demonstrate a more reasonable and fair approach to the problem? If you were the original tenants, would you appreciate an opportunity to make it right and retain your residence? Or would you cop the eviction even though you didn't personally do any of the damage?
Now if you did the necessary clean up and repairs, but you allowed the 'visitors' to come back and do the same things as before, then the Landlord, upon inspection, is not going to have a choice, is he?
By allowing us to make choices we are all facing the same inspection. Our relationship with God will ensure that we do not break the rules because we know it would incur his displeasure and result in our own eviction from God's property. We will not join in with what others are doing to this earth and to each other but will try to tell them the consequences of doing so. We will be doing all we can to keep the unsavory characters out of our own lives and not imitating or even condoning their behavior.
You could make the argument that God's condemnation is just, but if you believe he's going to come and mercilessly slaughter everyone that doesn't worship him then you can't say those people are condemning themselves. It's pretty clearly God that's doing all of the genocide, isn't it?
Its not like we have had no warning. Justice is served by warnings and when the warnings are ignored, then there will rightly be consequences.
We have known since the Bible was written that an accounting with our Landlord was coming. He gave control of the world over to the god that our first parents chose, in full knowledge of where it would take us....but we needed to see firsthand what happens when we throw God and his rules away. Do we need more evidence that this world's ruler and his rulership is a total failure?
We have had plenty of time to comply with God's requirements, but at the end of the day, only those who have complied, will be granted citizenship in the new world to come. That citizenship is not in heaven but right here on earth where God put us in the first place. Not a soul in that world will be an atheist, or a worshipper of false gods. So we have a choice as to whom we will worship and God knows the reasons for our choices. If we are missing from that world, it will be because of the choices we have made.
Loyalty to God comes out of love not fear or force, so if we love God, then his rules will never feel like they are unjust or unreasonable. We will be able to comply with the tenancy rules with no hesitation because we agree to them and we uphold them in spite of what others are doing.
That is how I see it.