Starting World War 3 would also kill innocent mutants as well as humans, does not seem practical to me.
The entire plot of
X-Men First Class was about Shaw wanting to instigate a global nuclear war so that mutants can inherit the post-atomic wasteland where the radiation will increase their numbers. Magneto throws away dozens of mutants he considers "pawns" in the Alcatraz fight in X3. He tries to kill his BFF Mystique because she represents a threat to mutant-kind. He has no problem killing Xavier's mutants. Clearly he's not above killing or sacrificing many of his own kind for the "greater good" of exterminating humanity and making mutants the dominant life on Earth.
Which is a good point I made myself.
In the third world, it's probably going to happen.
But the same tests that can notice Downs and other abnormalities, by the tech level seen in the first movie can probably look for the mutant gene as well once "normal regular" Doctors know to look for it.
For just 20 dollars well before the point you can no longer abort the pregnancy, you can can know definitively if there's a freak in your oven.
(I saw something similar set in the future after the gay gene was discovered and up %90 of parents discovering that their child would grow up to be gay, chose abortion and starting over again until they finally made a straight one, rather than continuing with their gayby.)
There's this thing that happens. Urban myth really, but crack whores are paid to have their tubes tied because they are pathetic and have no right to bring another baby into the world just to dump it into the system a day later when they can finally go looking for crack again.
I can see charitable foundations (the government) actually paying people (mothers) money, a hundred dollars, maybe a thousand, to abort mutant births. And then I can see the ghetto crack whores getting uppity that those Beverly hills skinny princess bitches are getting paid ten times what they are to abort their mutant babies!
(Not too different a principle than scratchers.)
(If the argument can be made by the Catholic Church that mutants do not have souls, does that mean that they are fine with contraception and abortion if you can prove that all to most of your children are going to be mutants?)
But once the "Cure" was discovered in the third movie, all bets were off. They could no longer subtly out breed humanity, if all children were then inoculated at birth or before birth.
Magneto and Kennedy were friends?
The Space Program?
Same principle as a rail gun, Magneto could have sent explorers to the moon in 1962 if the government was in good standing with him.