On the surface, you have a valid point. The space program, aviation in general, skyscrapers - they are all far more daring than anything Nimrod and his crew attempted. So, based on the statement that you quoted from Malachi 3:6, one would think that there would be an appropriate response from Jehovah.
You might say, too, that modern man has brushed off God more so than Nimrod and his bunch. The statement in Genesis 11:4 ("for fear we may be scattered over all the surface of the earth") seems to have them at least acknowledging the possibility that God might intervene in their affairs rather than blithely assuming that God will simply bless their efforts. (To me, that presents them as having a somewhat grudging respect for God.)
At any rate, I know some will cover the ideas that it is just a hokey story. I'll let them do that. I was going to offer a different possibility, that is, that the Genesis chapter 11 account does not contain the entire story about why God acted in the way He did.
As an example, the story about the defection in Eden in Genesis chapter 3 does not bring in any information about Satan the Devil. You have to read about that in other places. If the entire Bible is authored by just one person, namely God (many will contend that, but your question in your initial post presupposes that to be true), but if you accept that as a premise in your question, then, the reason for the omission of extra information has to be intentional. That is to say, God only wanted to say so much about it at that point in Genesis. Any seeming conflict in the way God has acted is just that. It only appears that he has acted in a contradictory fasion because of not being aware of all of His motives/reasons. Such misunderstandings happen between humans all the time.
I'll also add, that the commentary you heard in a public talk was just the speakers impression or opinion. Nor does the Society understand why God acted the way He did in Genesis chapter 11, beyond what the chapter says about it. I can say that because they haven't been able to answer the question you posed.