For long flights I either wear very comfortable shoes, or bring 'snuggle socks' to change into. I think going barefoot is gross, but sometimes you need to get out of your shoes.
Slipper-style socks seem the best compromise. I still slip my shoes on before heading to the bathroom though. Usually the bathrooms seem clean, but I'm not one to risk it.
I hope they will say 'no walking around barefoot' - it's gross, and what would happen if as you walked past someone they knocked their coffee over? Hardly safe...