Even in that scenario, it is very simple, we protected the people today and use vaccines to induce the necessary mutation. The moral choice in my book is to always err on the side of the living than "potential of the living".
For instance, the British military planners allowed soldiers to die on the battlefield, who they could have saved, in order to protect the secret that they had cracked German encryption during WWII. That was a place where the needs of the many, were deemed more valuable than the lives of the few.
I'm not judging one way or the other, but it has happened in human history more than once. And in the imaginary scenario where leaders had perfect knowledge of the future, it would likely happen again.
This is not a very good comparison, in my opinion. Military is rarely about the "needs of the many" far more than it is about the "powers that be". Once you understand the dynamic at a play, it is rather clear that the soldiers died for what soldiers almost always die for; the regimes that pushes them to war.
It's all academic of course, we'll never make such a decision, and never know what could have been. It's just another reminder that we don't really know the future or the best course of action in these situations -- we're just taking our best guess (even the experts).