Classes can act independently of jobs, and whats more is that Jobs incorporate classes. So I dont have a problem with it, and would love a thief class and ninja job combo. In fact, sometime in the near future I will flesh out an idea for just such a combo. Will the developers use my ideas verbatim? Doubt it. But it would be nice if it helped the cause of making such a combo, as well as the role I see it playing.

Also If its AF armor you are worried about and what not, they also said there would be class specific gear.