Seed on the inside of the fruit will not have any canker bacteria, since the bacterium is not systemic. But if the surface of the fruit is contaminated, there is some possibility that it could be transferred in the process of extracting the seed. Even so, the seed are going to be planted under ground, and I would not expect the bacterium to move up onto the growing top, as it emerges. The bacterium is not always killed by surface drying; if that were the case, it would be an easy disease to eradicate.
Rinsing seed in 5% Clorox solution for a minute or so should kill any bacteria that may be present on them.