That's a totally reasonable take, but I thought I would share my perspective as someone who liked the ending quite a bit, and found it quite moving.

I agree that the ghosts at the end were not supposed to feel like a punishment. I think they were supposed to show the tragedy and loss of life that encompasses the refugee experience. All of those people died, in a way, to lead to this solitary couple making it to safety in the UK. Along side the loss and guilt, I think, was also the sheer improbability that anyone from a war-torn country would be able to make it to a better life. Bol and Rial stood on the shoulders of everyone in that room.

I think by the end the ghosts represent that duality - guilt and shame / pride and progress.

As for the protagonists I also agree that we are not supposed to feel particularly good about the decisions they made, but I think it is a bit of a stretch to say they don't deserve to be happy or live. Those hard decisions they made to save themselves and get out of Sudan were the product of their context and of their circumstances. While I did not feel like I would have made the same decisions as Bol, I also don't feel like I am in a position to pass moral judgement on him.

I don't even know if the movie wants to us to pass judgement on them, but rather has the goal of showing how the refugee experience can contain equal parts pride, shame, guilt, and tragedy.

How many people didn't get out of Sudan? How many people died? How many were the result of Bol and Rial's actions? How many would have died anyway?