Barry would not have picked Miller. He picked him because he "gets under Johnson's skin". Who else would Barry have picked if he ran, as planned, against JFK?
No, Kennedy would not have dropped Johnson, which poses another scenario: Kennedy's health was pretty bad, especially his cholesterol. He was literally a walking heart attack. What happens if LBJ succeeds to the Presidency later, around 1967 with Vietnam raging?
As for Kennedy and Johnson, it is unlikely that Kennedy would have dropped Johnson in 1964. This would have caused turmoil and resentment in the Democratic Party, especially from the south.
However, in 1964, Kennedy would have been in a much stronger electoral position than he was in 1960, so if he had really wanted to drop Johnson, as unlikely as this would have been, he could have done it in 1964, and still have won the election handily. But there really would have been nothing to gain by causing turmoil in the party by dropping Johnson.
An alternate to Johnson could have been Senator Stuart Symington of Missouri, a choice many thought Kennedy should have made in 1960.
A more remote possibility would have been Senator Humbert Humphrey of Minnesota, who Kennedy defeated for the nomination.
A still more remote possibility would have been Secretary of Agriculture Orville Freeman, who was a former two term Governor of Minnesota, who had supported Kennedy for the nomination in 1960 when many in Minnesota were being urged and pressured into supporting Adlai Stevenson, and Freeman was someone who Kennedy thought highly of.