If I recall correctly, the idea was that JFK was a mutant, and Erik tried to bend the “magic bullet” to save his life. Which is bizarre for a whole bunch of reasons:

• First, the “magic bullet” theory is bullshit. It’s based on a misunderstanding of the layout of the car that JFK and entourage were sitting in.  

• Second, even if we accept for the sake of argument that Erik found out that JFK was a mutant and that JFK was going to be assassinated (which is never explained) and where and when that would happen (ditto), why wouldn’t he just stop the bullet, something he’s clearly capable of doing?
• Third, if JFK was a mutant, wouldn’t he have gotten way more involved when the Director of the CIA took a meeting with Xavier and found out that Shaw was behind the Cuban Missile Crisis? 
• Fourth, Magneto not dying would have changed U.S culture around conspiracies enormously, which would have had a significant impact on popular trust in government. We don’t really see any signs of this.