So I have considered if God tests us and if God punishes us through natural disasters. However the idea of God disciplining humanity in general is a bit different. In today's society, for anyone other than the parents to administer “discipline” in the form of punishing their own children is frowned upon. School authorities are delegated a certain degree of authority in that regard but physically touching the child is condemned.
The Bible uses the word discipline to encompass not only correction and chastisement, but also for gentle instruction. It is applied to actions God takes towards believers, not to those who are non-believers. This can be better understood when we realize that, in the Bible sense, discipline and disciple are related words. God's teaching and direction are intended to make us faithful followers (aka disciples) and therefore "disciplined" in the ways of righteousness. This is a teaching method that is usually gentle but sometimes much stronger. Perhaps the closest to this concept is that of an “academic discipline.” Obviously, non-believers reject any such discipline – teaching, molding, correction or otherwise.
However, even estranged imperfect humanity is God's creation (offspring of Adam), not just believers. God does not desire anyone to be destroyed but wants them to gain everlasting life. Both the proclamation Jonah was sent to deliver to Nineveh and the public preaching done by Christians today demonstrates that God does at very least provide warning so that those that heed the warning might live. Just as parents are known to warn a disobedient child as a form of discipline, in that sense God likewise disciplines before taking the next step. If those not obedient to God turn around from their godless ways (as in the case of Jonah’s Nineveh), God is merciful. If however, they reject even the warning, it will turn out badly for them, just as in the days of Noah.