To choose the rhythmic variation you are going to use, you should take a look at the whole song to see where the syncopation points of the melody are located. If you look only at the first measure you may be fooled depending on how the melody begins.
See that I used a different rhythm pattern in the first measure of the intro and also in the first measure of part A (the melody is in fact at downbeat, you are right). However, if you look at the next measures, you will see that the syncopation points of the melody match the rhythm I used.
Listen to João Gilberto playing the same rhythmic pattern I used in the first measure of Chega de Saudade in this recording of Wave, from 20s