S.J.
I never understood people who get all worked up about people touching their babies. Don't get me wrong, if your child is a preemie and has health issues, no one should be touching that baby. But a healthy six month old at the store with super cute fat cheeks just waiting to be pinched, well that is just asking for it!! =)
Seriously though, these sweet old people just love babies, and your daughter has the ability to make their day just with a few minutes of your and her time. Try to relax. Spray her down with lysol when you get home if it really worries you that much....
And no, I don't think it is rude at all for you to simply say after a minute or so "sorry, we are in such a hurry, thank you for your kind words about my little girl, but we have to go!"
ETA: Sounds like it is just your "thing" - and that is OK! We all have them. Some people are just more thingy than others. My husband FREAKS out if I grab a piece of food off of his plate. I couldn't care less if someone does that to me. So to me, his behavior is odd, but hey, it is his thing!