Yeah, especially because Kennedy is generally a well-loved and iconic president. His portrait can still be seen in some American households, and for some people who can't separate reality from fiction, the idea that Magneto (the "cool" one) did it will surely be an "issue", lol.
Personally though, I believe BOTH Magneto and Mystique are innocent. Kennedy was a liberal and apparently pro-mutant, so there's no reason for Erik to do it or to order anyone to do so. I'm pretty sure Magneto was trying to stop the bullet after the first shot was heard, and then likely got sabotaged by someone (a telepath messing with his head? Wanda-like powers? A telekinetic?). Anyway, it altered the trajectory of the bullet.
I think Magneto chose to turn himself in so that everyone would finally know about mutants once and for all, and then denied the crime and pointed his fingers at Mystique because he knew that with her abilities, she would never be caught anyway.
I'm pretty sure the truth of the killing will remain as it is as we know it here in the real world. Meaning, the "real" masterminds unknown and the "magic bullet" remaining a mystery.