Pasteurization does kill helpful bacteria along with any pathogens, and it also destroys vitamins (Kilshaw et al 1982). And also see wikipedia.
Other than the effect of pasteurization on the milk per se, it is worth considering the health of the cows. Raw milk is more likely to be available from small herds that are pasture grazed, and more easily obtained fresh. By contrast, most of the pasteurized milk available in the store comes from large dairy farms that have as many cows producing as much milk as possible, and standard practices used to increase production include regular doses of antibiotics, hormones, and corn/soy feed. So pasteurized milk starts off less healthy before it is pasteurized. Add to that the effects of storage and it is clear that, in the absence of any pathogens, raw milk is healthier.
Pasteurized milk also spoils, whereas raw milk transforms (e.g. to yogurt, cheese, etc) as it ages.
The problem with raw milk safety is that it doesn't scale well (Steele et al 1997). Although I do know a local goat farmer who I trust and from whom I purchase raw milk, it is difficult to know the safety of milk from unregulated dairies. Knowing the farmer and the conditions of the herd provides valuable information. The one source of raw milk that I fully trust and think is likely safer than pasteurized milk in the store, based on their own self-regulation that includes much more intensive testing than required by the USDA, is 'Organic Pastures'. Their website is a good resource for information on raw milk, and I believe that they ship.
Furthermore, it is worth noting that there have been plenty of listeria and salmonella outbreaks from pasteurized milk sold in stores.
P J Kilshaw, L M Heppell, J E Ford 1982. Effects of heat treatment of cow's milk and whey on the nutritional quality and antigenic properties. Arch Dis Child 1982;57:842-847 doi:10.1136/adc.57.11.842
Steele et al 1997 Survey of Ontario Bulk Tank Raw Milk for Food-Borne Pathogens
Journal of Food Protection, Volume 60, Number 11, November 1997 , pp. 1341-1346(6)