Um, no. Setting it on the counter at room temperature won’t pasteurize milk. You need 160° to 165° for 15 to 30 seconds. It does affect the nutritional value, as it alters the composition and makes it harder to digest. It kills the beneficial bacteria along with the pathogens.
Yes, raw milk has bacteria, good and bad. There are potential health risks, but also benefits. For many people, the benefits outweigh the risks. I cannot drink pasteurized milk without becoming physically ill for a day or two, unless I also drink raw milk around the same time, which counteracts the effects of the dead milk. So my personal experience reinforces what the scientific facts tell us.