M.P.
I wouldn't be concerned about putting his pacifier against the corner of his eye or rubbing it on the rim. The pacifier is soft and edges are rounded and won't injure him. Your son will not purposely hurt himself.
If your husband is concerned about germs, give him a clean pacifier. However, the more we allow our children to be exposed to germs the healthier they will be. I'd only be concerned if he or another member of the family has a cold. You don't want to introduce cold germs into the eye. However, even then, I wouldn't be overly concerned. We do introduce germs into our eyes every time we rub them with our hands.
Rubbing his eyes with his pacifier is really not much different then rubbing them with his hands.
This is normal behavior.