In the second image here [1] there's a security seal on the payment closure as a whole; I'd imagine a simple security seal along the side of the card scanner intake would thwart most would-be card skimmers, no?
At that point the employees could just make it part of the standard inspection and it'd be more obvious to customers if they were missing.
[1]: https://cdn.sparkfun.com/assets/learn_tutorials/6/9/4/Gas_Pu...