I have to assume that the bacteria wouldn't survive cooking. Indeed, a reason for cooking is to kill off the stuff that makes us sick. I have even heard it argued that humans are by nature vegetarian. Reason cited: we can't reliably eat raw meat without getting sick. Not sure if this is true--and the person making this argument was clearly a firm vegetarian--but it gave me "food for thought."
But one advantage of having chicken with lower bacteria counts is that there is less bacteria to potentially spread around the kitchen. Although, of course, one should always be careful with cleaning, regardless of what type of chicken one cooks. (As mentioned before, at the moment I'm pretty much entirely on a vegetarian diet. One more reason: it eliminates all the worries and hassles of pathogens in meat. These days, living alone, the easier I keep things, the more likely it is that I'll actually cook from scratch.)
