I like to think of the 'If history has taught us anything, it's that you can kill anyone' comment on a less specific scale, more as a profound truth.
It always makes me think of the Roman emperors who were assassinated - who would have thought you could do that? But you could. All throughout history, prominent men of power have been wiped out despite their security precautions and heightened awareness of danger. Michael, it seems to me, might be looking at it from this point of view. After all, he's both a college boy and a soldier in the Marines, and as svsg said, he broke every rule in the book when he, as a civilian, murdered a police captain and a notorious gangster. What's more he has had first hand experience of the un-killable being killed; the assassination attempt on his father, an innocent sicilian peasant girl, the heads of the five families, etc etc.
I think FFC knew the comment would ring true for us because we had since experienced the assassinations of JFK and so many others, but I don't think this was necessarily a specific reference to one president.
A further use of this comment is, IMO, to foreshadow Michael's tragedy. Because Mike isn't just talking about Roth, Kennedy, McCluskey here. He's revealing his potential, the depths to which he will sink, in terms of the murder of Fredo. When he asks Tom if he will come along with him in 'these things he has to do', I always get a shiver thinking that he is introducing to Tom the idea of killing Fredo. Fredo didn't know, but Tom did. We see this as Tom pauses before entering the meeting, to watch Fredo with Anthony through the window. (I feel this mirrors the scene in Part I when he goes back into the house and watches through the window as Tessio is taken away.) The following scene is Michael testing Tom's loyalty in the face of the atrocious thing he is now asking him to accept.
The other part of the tragedy is the ironic use of this comment. Yes Michael, anybody can be killed. Just remember that when you're standing on the steps of the Teatro Massimo.
