God can be in control of the grand story arc without overruling the free will of man. In the same way that "luck is when preparation meets opportunity" blessings and cursings can be defined much the same way. God places opportunities in front of people and, depending on their preparation, they succeed or fail in those opportunities.
Giving man free will doesn't mean that God operates like the clock maker (above and outside his creation while no longer affecting it) any more than saying "God is in control" means God is wrestling man's will out of his hands as he sees fit.
In response to your examples, at least some of those (physics, biology, disease, medicine, etc) were put in place by God and it is up to man to find them. What have we actually created in this world that didn't exist before and just had to be forged or combined in a certain way? Opportunities that God provided and people seized.
I'd point to a handful of scriptures like "there's nothing new under the sun" (Ecclesiastes) or "through him all things were made and without him nothing was made that has been made" (John 1) but the general theme of your post is asking me to interpret something that God has not explicitly revealed and requires a certain amount of inference and cross-reference so I can't site a specific passage.
**Bonus Material** I'd contend that God has not ever wrested the free-will of many away even in instances like with Pharaoh. He controlled the words of Moses mouth (Exodus 4:12) he saw the pride in Pharoah's heart (Exodus 5:2, 1Sam 16:7) and he used the words of Moses to exploit that weakness. Opportunities and preparation...
Just my 2 cents
Sic'em