The point of the scene with Jonathan Kent is not that he is correct in suggesting Clark should have let the children die (I watched it again very recently--the more I see it, the less problematic it becomes). The point is he (Jonathan) doesn't have a definitive answer to a very big question--and to a more immediate one. Let's leave aside the "ramifications of answering the question of 'are we alone in the universe'" and consider a far more intimate and immediate concern. Jonathan and Martha are, first and foremost, thinking like parents--not moral adjudicators for humanity. It is a more overtly cynical and paranoid world today than the 50s. They would be delusional NOT to think the government would swoop in to take Clark away if he "went public". He's what, 12-14 in that scene? If my kids had powers like Clark (they don't--just typical 10 and 14 year olds), you bet your ass I wouldn't want them to "go public" at that moment and I would DEFINITELY have a selfish reflex, if only for a moment, where I might say something similar to what Jonathan says to Clark. Such a reflex is entirely understandable on the part of a parent--for whom the safety of his own child is paramount. There is precious little I would not do to protect my children, at the cost of many of the values I hold dear. But anyone who thinks Jonathan is just blithely endorsing the death of a busload of children, with no indication of how horrible that would be, is misinterpreting the scene, both in purpose and performance. Jonathan has a human reaction, weighing the safety of his only child (adoptive or not, makes no difference) against the lives of others for whom he has no direct responsibility. His is not a "fuck 'em, let them die" attitude. Not in the least. And frankly, it is beyond baffling to me that anyone would read the scene in that fashion. Again, one can be disappointed the Kents are not the "paragons of virtue" they are usually made out to be. Nothing wrong with that disappointment. But such disappointment does not justify twisting the scene (and many others, as I've seen done in many instances) into something it plainly is NOT, just to make one's disappointment clearly heard.That's the problem with pretending things are more complex and cynical in today's world. You can justify any bad decision in the movie as "this isn't the 50's" and pretend that makes it better.
In the real world, some things really are black and white. Saving a bus full of innocent children from dying has no moral complexity. You do it, and then work out the ramifications later. Same with saving your father. There are absolutely zero situations where trying to do this isn't the right thing to do.
The fact that some people can find any justification in pretending this is a morally grey area is almost scary.