> the problem remains that God watches it being perpetuated.
Yes, He does. And He is constantly at works in ways that He can work to eliminate or reduce it. The Earth continues to produce abundantly. People all over the world work in both coordinated and parallel efforts to bring food to the hungry.
> Why is preserving the freedom of the malicious force more important than the freedom of those that share?
I don't think it is. Any "freedom" has to work within the constraints of morality, responsibility, and ultimate good. Some people, however, see freedom as the right to do whatever I want, but civil freedom can never responsibly be interpreted in that way. We can't allow "freedom" to murder, rape, steal, etc. Nor should we allow the "freedom" of malicious force.
> This is essentially the result of God standing by in these cases
God doesn't stand by. He is continually at work in the lives of government leaders, military forces, police, courts, lawyers, advocates, social services, and individual people to effect righteous change in the world. God works through His people.
> "All it takes for evil to prevail is for good men to stand by and do nothing."
Right. That's why we don't. We are constantly at work, by the power and will of God, to effect justice, compassion, health, and peace in the world. Constantly. God is at work in us and through us.