I think when we talk about control we have to understand it in the proper context. There’s control in the sense of “government” vs. control in the sense of “marionettes”.
God doesn't control in the sense of pulling the strings of we puppets. People are free to choose to be for or against God. No, God controls in the sense of governing in accordance with his will (i.e. his policy)...and because he’s sovereign, his will/policy is absolute and will be enacted regardless of one’s personal choices.
Let’s look at the story of Jonah for a moment.
God said,
“Jonah, I want you to go to Nineveh and tell the people I’m going to destroy their city because their sin has risen in my face.”
God’s policy was to cleaned up Nineveh because their sin had risen to the level of extreme offence that it must be eradicated one way or another. God’s will was to destroy Nineveh’s iniquity...and his will is absolute. It will happen. Nineveh’s iniquity will be destroyed one way or another either by purifying the people or toasting the city itself.
God in his authority charges Jonah with the responsibility of effecting the clean up.
Jonah says, “Nope.”, and then flees in the opposite direction. This was completely Jonah’s choice. Jonah was in full control of his actions.
Now imagine what’s going on in Nineveh during Jonah’s rebellion...Things must be either as bad or likely getting worse because Jonah’s not there. But this doesn’t mean God isn’t governing the situation. He’s not slow (as some people would count slowness). God’s remedying the situation but God’s not going to send another agent because he – in his complete authority – charged Jonah with the task. And if he were to pick someone else that would suggest Jonah is outside God’s governing authority.
So who’s in control of what? Well Jonah’s in control of his decisions, but God’s in control of his government policy involving both Nineveh and Jonah. So Jonah has the choice to yield to policy or face the consequences.
Jonah freely refuses his commission and God sends a terrible storm to destroy the ship he was a passenger on. It’s God’s government so he can do whatever he wants in full sovereignty. Jonah relents and chooses to be cast overboard and is swallowed by a large fish (sent by God) for 3 days & nights. This whole ordeal was misery for Jonah. Finally, Jonah is spit out on the shore and once again God commands Jonah to go to Nineveh.
Jonah chooses to go to Nineveh and Nineveh repents of their sins. God’s policy was still enacted through Jonah, even though Jonah freely chose to rebel against God. Now if Jonah had gone to Nineveh and they still refused to repent, God would've destroyed the city completely and it still would've been God's will/policy: Nineveh's iniquity must be cleansed one way or another.
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Hopefully this shows the dynamic between man’s free choice and God’s sovereignty when talking about control. There are people suffering in the world, as well as evil conspiracies hatched by evil people that harms others, and God is quite aware of it and is governing the situation. He is not slow to act as some people would count slowness, but rather patient. And there are agents he’s commissioned to fix the situation who are currently being prepared, or they’re prepared and freely choosing to be stubborn for the moment like Jonah. But guaranteed; God’s making it “rough as the seas” for these stubborn folks until they realize they can’t hide from their duty. God’s policy will be enacted through them. Meanwhile the record of the selfishness and evil of others is being recorded in heaven counting as a time of God's mercy before judgment on them.
Hebrews 12:6
For the LORD disciplines those he loves, and he punishes each one he accepts as his child."
And he knows his agents will come around because he knows them; he knows the character that’s within them. It’s his character. They’re his children after all. And as sure as he knows himself he knows those with his Spirit will enact his will/policy.
Zechariah 4:6
"This is the word of Yah to Zerubbabel: 'Not by might nor by power, but by my Spirit,' says Yah of hosts.
So truly, God's governing the situation, but what we're experiencing in the interim (which can be frustrating) is God's great patience. But persistently cry out and pray for justice as Christ says to do, and that justice will come more swiftly (Luke 18:1-8).
