The fundamental fallacy that is being comitted here is that we do not need to flesh out the perfect balance between intervention or not to figure out some extreme cases. For instance, when should we intervene in other parents parenting? we cant make a perfect standard, but that does not prevent us from making the clear and solid judgement you should intervene if the parents are having their children locked in the basement.
For God's case, it's different. We can't hold him accountable. In the beginning, we asked for autonomy and we got it. He doesn't have to respond to us. He isn't accountable to us. We are accountable to him. It is he who would ask why we allowed what we allowed. Given that we were capable of stopping it, we would be inexcusable.
God is hands off. For now, we do what we can and deal with the consequences, whether good or bad.
You are still relectant to deal with the fact that there are, indeed, many examples of the very extreme cases you advocate for intervening with. WWI & II come to mind. In all those cases, it is a human problem, something of our choice. Eliminating these sources of suffering, while being great in the now, wouldn't alleviate the core problem. We still want to do whatever the hell we want! We don't want to be told what to do and not to do.
Let me turn this on you now, and see how you would respond. You are pro-choice. Why aren't you intervening for the life of that innocent child in the womb? Does that mother have autonomy or not? Please, don't chicken out. I know this is a hard one.