I believe booties are the blue, medical style things meant to be worn over shoes in sterile settings.
IME, these are designed more to keep any dirt, dust, bacteria, etc on one's shoes from getting on the floor, not really to keep the grunge from the floor off of the shoes. Maybe they do that as well... I don't know.
So far I like the disposable flip flop idea. I bet one could purchase a bunch of those post pedicure flip flops fairly inexpensively to be used at checkpoints. I found some
here for $0.40 per pair. ($40 for 100 pair)
Here's another site that has 12 pair for $4.80.
Another site selling 10 pair for $6.65.
More, including paper slippers, 100 for 15.99.
This site seems to have the best prices... lots of different kinds.