You're overlooking the issue of rhetoric. Kennedy took a hardline stance during the campaign and in the early part of his administration, which forced Khrushchev to reciprocate to keep his own hardliners off his back. Americans have built up such a mythology around JFK that it's easy to forget how frightening his "missile gap" talk must have sounded to the Soviets, who knew full well that the Americans were already outproducing them.