Doesn't sound plausible. The B-58 did once hold the record for distance (8000+ miles, Tokyo to Britain, in 1963), so 2 or 3 could have made the trip. But I doubt they would have been able to outrun the inevitable interceptors the Russians would have launched along the borders to meet the returning B-58's.
Remember, (not that Kennedy couldn't have called Khrushchev on existing lines), the "hot line" was not installed until 1963 as a result of the Cuban Missile Crisis.
But, the biggest issue of implausibility has to be in the idea Kennedy would authorize such an incredibly audacious act when the whole world teetered on the brink of nuclear war. Khrushchev was not one to be taken lightly - perhaps the sight of B-58's over the Kremlin may have pushed him to launch missiles from Cuba or made him back down, but it doesn't sound like a likely bet anyone would have elected to take at such a precarious time.
The more likely story is as follows from
http://www.gwu.edu/~nsarchiv/nsa/cuba_mis_cri/moment.htm
"The second volume of Khrushchev's memoirs (Khrushchev Remembers: The Last Testament), published posthumously in 1974, touched only briefly on the Robert Kennedy-Dobrynin meeting, but included the flat statement (on p. 512) that "President Kennedy said that in exchange for the withdrawl of our missiles, he would remove American missiles from Turkey and Italy," although he described this "pledge" as "symbolic" since the rockets "were already obsolete."
Over the years, many scholars of the Cuban Missile Crisis came strongly to suspect that Robert Kennedy had, in fact, relayed a pledge from his brother to take out the Jupiters from Turkey in exchange for the Soviet removal of nuclear missiles from Cuba, so long as Moscow kept the swap secret; yet senior former Kennedy Administration officials, such as then-National Security Adviser McGeorge Bundy and then-Secretary of State Dean Rusk, continued to insist that RFK had passed on no more than an informal assurance rather than an explicit promise or agreement.
The first authoritative admission on the U.S. side that the Jupiters had actually been part of a "deal" came at a conference in Moscow in January 1989, after glasnost had led Soviet (and then Cuban) former officials to participate in international scholarly efforts to reconstruct and assess the history of the crisis. At that meeting, former Kennedy speechwriter Theodore Sorensen (and the uncredited editor of Thirteen Days) admitted, after prodding from Dobrynin, that he had taken it upon himself to edit out a "very explicit" reference to the inclusion of the Jupiters in the final deal to settle the crisis."
Another good source (no mention of B-58's over the Kremlin) is http://www.coldwar.org/index.html
The first authoritative admission on the U.S. side that the Jupiters had actually been part of a "deal" came at a conference in Moscow in January 1989That may be the case, but the de-facto deal was obvious and reported on as such, shortly thereafter, when the Jupiters were in fact removed.
As for the B-58 story, I don't buy it. That would have been out of character for Kennedy, a cautious person, who deliberated slowly in making decisions. And there was way too much uncertainty at the time as to USSR's intentions. Such a provocation, if detected, could have resulted in a disastrous nuclear exchange, for no good reason at all. Sounds like a Kennedy-philiac wetdream to me.