Much of what humans naturally like to do is destructive and harmful to others, and yet we see fit to convince each other to stop. We naturally like to form tribal associations and prejudge people by their membership or lack thereof, often with violent results. But nobody says we should just let it be since that's what humans evolved to do (well, nobody worth paying attention to). I fully agree that we are unlikely to ever stop reproducing. But that's a question about practicality and real-world feasibility, not morality.
I'm of the opinion that moral systems aren't a construct of human will, but of physical reality. At any point in history there could have been no other way, and at any point in the future the same will be true. What ought to be is usually what happens eventually. For instance, slavery and violence is on the decline, democracy is on the rise, and so on. Society tends toward increasingly morality, and that's all that really matters.
So how do you know that future people won't come to a moral conclusion that favors extinction? If they do, it would have to be a case of discovering something that was always morally true, according to your reasoning (after all, it's not like slavery only started being wrong when society came around to realizing it). To say that we are working toward a future morality that will be more accurate than the current one is not to say anything about what that morality will look like.