I have owned my own Child Care Center and have over 15 years experience. My insurance would have had a fit if they knew I didn't have kids wearing shoes at all times. Some child care places won't even let kids take their shoes off for nap time in case of a fire. Having to stop and put kids shoes on to get outside is a useless waste of time.
Although I think it is a good idea for kids to not track stuff in, usually sand from the playground, I would never expect kids to walk in pee and poop, much less where other bare feet have walked...kids get athlete's foot too. I think only wearing socks is nasty too. Socks getting dirty shows you what is on their floor. Sock absorb the substances on the floors and hold it next to their skin until the socks come off. Ewwwwww!!! Kids sit on those floors, put toys off the floor into their mouths, some even lick the floors.... I know my carpet in the circle time area was always getting dirty. Kids track paint, sand, dirt, leaves, animal poop from the sand area, you can imagine what else. A center can't clean their carpets every day, not even monthly. It's just not affordable or practical. Most do the best they can.
DHS requires child care facilities to follow certain guidelines. If your place is licensed then you can look up their past inspections. The link is listed below.
http://204.87.68.21/childcarefind/
Here is a link to what child care centers are required to do:
http://www.okdhs.org/NR/rdonlyres/C###-###-####-C005-45D1...
You may also want to call DHS and ask for a licensing worker to discuss this facility so you can find out if they are able to tell her she can't wear shoes.
Here are the phone numbers and contact information.
http://www.okdhs.org/divisionsoffices/visd/dcc/ccl/docs/r...
Keeping kids areas super clean/sanitized is something that is nearly impossible to do. Kids need to be exposed to germs to build their immune systems. If the place you are taking your child is a place like a Mothers-Day-Out then they are going to fall through the cracks. You will have to decide if it is worth your time to take your child there. You may be able to find a different place that allows her to wear her own shoes. If you really like this place then by all means ask them before spending money on socks they won't let her wear.