You're right in noting that the naturally occurring bacteria are destroyed in the pasteurization process, so what might be contributing to souring or curdling milk that has been pasteurized is unknown and could be something risky that has been introduced. Cooking well (using the soured milk in a cooked product) would most likely destroy any pathogens that have grown but there is always the risk of cross contamination in handling, so we suggest not handling obviously spoiled products any more than necessary to discard them. It is likely that off-flavors would develop anyway, and make this a very undesirable product, even as an ingredient in a cooked or baked food,  

We recommend against using raw milk products. However, if raw milk has soured, it has better potential to be an ingredient in a cooked product, but should never be consumed with out careful pasteurization or fully cooking as in ingredient.  

Hope this helps.