Well, one thing that I do know is that lactose intolerance is incredibly rare in babies, while milk intolerance/allergy is very common. So, for that reason alone, I almost always suspect milk over lactose. Babies can have temporary problems in breaking down lactose after a tummy bug, as the enzyme (lactase, I believe) that breaks down lactose is very low when suffering from a virus and it can take a few weeks to build back up.
I do believe that symptoms are fairly similar. Most babies do NOT like the taste of hypoallergenic formula, it's quite bitter and I'm sure you can tell from the smell that it is very different than regular formula. It will take him a while to get used to it but do persevere. We mixed our regular formula with the hypoallergenic stuff for AGES before DS drank a full bottle of it - we just decided that getting him used to it slowly and dealing with the milk problem was better than pushing it on him and having him not eat, be hungry, etc etc. Your LO will eventually get used to the taste and believe it or not, ENJOY his milk once it is no longer upsetting his system and he is used to the taste.
Could be a lactose problem, but my first instinct is to stick with the Alimentum if your doc is suspecting a milk intolerance.