Not at all. Read more carefully.
The 1948 convention barely passed its civil rights plank. The party as a whole wasn't exactly unambiguous on the point, and would have lost even more Southern EVs if it had been anything but.
Several decades of political history suggest that the subject of civil rights remained controversial within the Democratic Party for some time.
The point is that black voters in general and even Southern blacks in particular were crucial parts of both Truman and Kennedy's winning coalition, so it's completely ridiculous to argue that either candidate benefited from Jim Crow voter disenfranchisement.
In fact some people argue that black voters put Kennedy over the top in Missouri, Texas and South Carolina. (This thread has made me spend too much time researching African American voting patterns in the South.)