For someone who collaborated with the Nazis, (albeit not for their ends, but his own) I think he knew well the dangers that mankind could inflict on a minority population if they put their minds to it. Thus, instantiating a nuclear war serves two ends. Firstly, it disables the human power structure necessary to mobilize a global mutant extermination effort. In the "best" case scenario (for humanity) you have the Soviet Union in shatters, the U.S. not totally destroyed but hurt, and the global economy in one hell of a mess. In the worst case scenario, you have environmental damage that obliterates civilization altogether but not humanity as a whole. Either way, nobody is going to be able to organize against mutants for a long time, allowing them the opportunity to become the majority in relative safety from humanity. Secondly, per the belief that radiation can accelerate the activation of the X-gene you get a surge of new mutants from the surviving population in a short amount of time.
So, yeah, a lot of current mutants would die, but Shaw was looking at the big picture. His aim was to assure the survival of mutant-kind, even if that meant he had to sacrifice the majority of living mutants to accomplish that.
Imagine a fictional scenario where aliens have landed and although they haven't attacked yet, you strongly believe that they will and when they do all of humanity is likely to be wiped out entirely. You can wait for that to happen or you can take preemptive measures by launching the world's nuclear weapons at that them. If you do the latter most living humans will die, but all aliens will be gone, ensuring that the human species will go on. Do you decide to launch the nukes? If you're Shaw, the answer would be yes. And, although it's not an exact parallel, that was his reasoning behind his decision to instigate a nuclear war.
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