i am sure people today are prideful enough to challenge God, and sure also that no one has ever been capable of truly challenging Him, even tho they have from the beginning.
Nimrod, a mighty hunter of men, was building a fortress at Babel to make a name for himself. he was worshiped as 'Marduk' and the constellation we know as Orion was named for him. he was an extraordinarily powerful man, called a mighty one, similar to the nephilim before the flood. tradition among the Jews is that when Esau sold his birthright to Jacob, he was on the run from just having killed Nimrod - explaining why he said he would die if he did not get some stew. he was not planning to stay at home; he was being no doubt pursued by Nimrod's men, in fear for his life.
so what kind of things was God preventing by confusing our languages? would we be able to overthrow God?
absolutely not! but what kind of man is this Nimrod, who built Babel? he and his people would have gone on to do extraordinary evil on the earth, if God had not 'handicapped' us this way.
yes, this is for our good - just like it is for our good that we do not live hundreds of years anymore: to keep us from becoming as wicked as we would if we were left able to be.
i wouldn't be too sure that it's only Christians led by the Spirit that are recognized and persecuted by the world. there are a lot of people who seem to think that whatever they do, as long as the world condemns them, that is evidence that what they are doing is right.
and i wouldn't be too sure that every Christian led by the Spirit is recognized and singled out by the world, either. while it's true that the world will hate us for His sake and it's 'woe when all people speak well of you' it's not necessarily the case that the world even takes notice of Christians walking in the Spirit - if i do spiritual things but the world can't discern spiritual things, isn't it possible they don't recognize what i do? and in addition to this, people who are walking in wisdom and love, by the Spirit, may be regarded widely even among the world with respect for their gentleness, their understanding and their compassion - such respect is a blessing from God - because as Paul wrote, 'against these things there is no law'