JFK wouldn't have lifted a finger for him. JFK, for a minor unimportant Texas court nomination, embarrassed Johnson by ignoring his pick and picking his own candidate. When Johnson when to the Oval Office to ask Kennedy to change his mind, Kennedy just turned his chair around and had Bobby explain to Johnson why it could not be reversed. And that's just one example of them not personally much caring for each other. After the Cuban Missile Crisis, JFK said the people who he trusted most during that crisis was Secretary Dillon, Secretary McNamara, Bobby Kennedy, and someone else. No mention of Johnson at all. Finally, you can't just separate the conflict between Johnson and Bobby as being completely unrelated to his conflict with JFK. Bobby was seen in many ways as speaking for the President. They often worked as a team where the President would sit back as Bobby did the pushy work for him.
But yeah, long story short, Johnson is on his own and I don't think the Vice Presidency is enough to save him.
Where is this example of Kennedy turning his back on Johnson, who cites it?
I'm not separating conflict between Johnson/RFK and Johnson/JFK, more that JFK was far more amenable and able to work with LBJ than RFK and saw LBJ's benefits. It's true JFK didn't rate Johnson's management in certain areas (e.g. space council) but it's not enough to justify a burning hatred as you say