I would just continue with what you're doing. He's learning to care for our planet and also learning about germs and good hygeine.
My 4-year-old daughter loves to "clean up our neighborhood", so we take a bag with us a couple of times a week when we walk the dog. When this started, I made sure she knew not to touch broken bottles or cigarette butts (the butts are probably not that much worse than other garbage, but they're disgusting and I just don't want my baby to touch them!). I also keep a pretty close eye on what she's picking up and what kind of garbage is in front of us. If it's too gross or dangerous, I'll ask her to either leave it or let me pick it up.
Since our garbage-collecting sorties are almost always limited to the time we are walking the dog, it's easy for me to wash her hands when it's over. If you can't wash immediately after a garbage-collecting session, the hand sanitizer is a great idea. He may be a little young for this yet -- because it takes at least a few days to complete, but there are experiments where you actualy grow bacteria from your hand, kitchen sponge, doorknobs, telephone, etc. by touching a surface. Someone below mentioned an apple experiment; I've seen it done with sliced bread as well. We touch some pretty nasty stuff every day without even realizing it.
You're doing a great job with your young man!