Could you elaborate on "alert readers" about McNamara? Let me elaborate what I mean. I hadn't planned on giving an alert, but simply having the President make the announcement. My characters don't know JFK's inner thoughts.
Again, I'm not trying to dictate what you write, just suggesting you firmly establish the nature of the story early, when readers are first setting their expectations. You don't need to use McNamara, I was just suggesting another alternative, but if you did chose to go that route, you wouldn't even need to flesh it out, just establish that you're not following the established history.
"You know, I really don't like that McNamara fellow. He's too ... militaristic."
John chuckled. "Neither do I. We both have different ideas about how to conduct foreign affairs. Don't worry, though, I've got different plans for him, but the time isn't right to switch his position yet. I need him waiting in the wings for now, ready to take charge when the time comes."
Again, that's probably too specific, but it illustrates how you can merely allude to different events playing out over time, rather than focusing on the most central one in most people's memory. But establishing that this story is not purely historically accurate, without labeling the story as "alternate" anything, should steer you around any misperceptions.
Edit: Adding warnings to books is akin to TELLING the reader what the book is not about, instead of allowing the reader to discover the story for themselves. I tried that myself, despite warnings from others, and it came back to bite me, so I speak from experience. It's generally better to weave such details into the story early, rather than leaving confusions to fester over time (he says, despite leaving plenty of confusing segments in his own stories to leave surprises later on). 'D