As HealthBites as already mentioned the evidence seems controversial, at best.
There is an article on the ScienceDirect site, "Does homogenization affect the human health properties of cow's milk?" and although the article requires (free) registration to view the full article, the abstract is easily available . Here is an excerpt from the abstract:
"During the processing of marketed milk, homogenization reduces fat droplet size and alters interface composition by adsorption of casein micelles mainly, and whey proteins. The structural consequences depend on the sequence of the homogenization and heat treatments. Regarding human health, homogenized milk seems more digestible than untreated milk. Homogenization favors milk allergy and intolerance in animals but no difference appears between homogenized and untreated milk in allergic children and lactose-intolerant or milk-hypersensitive adults. Controversies appear regarding the atherogenic or beneficial bioactivity of some casein peptides and milk fat globule membrane proteins, which might be enhanced by homogenization. In children prone to type I diabetes, early cow's milk consumption would be a risk but no link was observed in the general population and the effect of homogenization has not been studied. In the current context of obesity and allergy outbreaks, the impact of homogenization and other technological processes on the health properties of milk remains to be clarified."
Finally, I have included a couple of passages from Wikipedia on this topic: "Those opposed to homogenization argue that decreasing the size of fat globules may have unhealthy effects, including allowing steroid and protein hormones to bypass normal digestion and increase their levels in the body. Concerns that uptake of the protein xanthine oxidase is increased by homogenization, leading to hardening of the arteries (atherosclerosis), were raised in the 1970s. Subsequent research "failed to substantiate, and in many cases has refuted" a plausible effect of xanthine oxidase from homogenized milk on cardiovascular disease." 
"Kurt A. Oster, M.D., who worked during the 1960s through the 1980s, suggested a link between homogenized milk and arterosclerosis, due to damage to plasmalogen resulting from the release of bovine xanthine oxidase (BXO) from the milk fat globular membrane (MFGM) during homogenization. Oster's hypothesis has been widely criticized, however, and has not been generally accepted by the scientific community. No link has been found between arterosclerosis and milk consumption."