Well they could have handled the ending like that, but in my opinion, the movie is so relentless throughout (especially the final stretch) that their really needed to be something of a payoff, they needed that hopeful ending to the proceedings.
I was suprised that the baby was born a fair stretch before the end, but I think it actually worked. There were numerous moments when the baby was put in jepordy that allowed for some great, edge of the seat stuff.
I understand what you mean about how it would have been interesting to see what would have happened if these desperate, futureless individuals were actually responsible for destroying a miracle, but I think the baby needed to survive. However, I would have liked a less decisive ending. I personally think that the arrival of the human project was a little too happy an ending. I would have much rather have seen Theo dying, happy that he's done as much as he can and is passing something on witht he baby being named after his dead son, and that be it. It would have made a much better ending (IMO) if Kee and the baby were just left adrift in the boat, so the audience could contemplate whether or not they actually were rescued.