1. Buy shoes that aren't hideous looking inside
2. Lysol
3. Shoe trees for at least 5 days
4. Enjoy, my feet (and yours as well, I'm sure) have been in much worse places.
Everyone who has visited/seen most production and shipping facilities will know that pre-owned items of clothing and shoes may very well be cleaner than those you buy in a shop.
I would say if one would never buy used, there is no need to buy new either. The stores do not throw out the shoes after they are tried on by who knows how many customers before they are purchased.
I bought these in an eBay auction recently. Paid about $300. I could never get shoes like this at that price any where else. I'm sure everyone recognizes that these are Edward Green Chelseas.