1) Encrypt the traffic.
This is actually quite a pain, as you either need to authenticate the card and reader to one another or use a pre-shared key that you keep very careful watch over.
You're best off buying in a solution here; SIM cards seem to have been very successful, and MIFARE contactless payment cards I know offer a DES-based secure system.
2) Watch the insertion point.
ATMs are classically vulnerable to this, and are acquiring more security cameras to watch for skimmers and other attacks at or near the ATM.
Trying to detect a passive skimmer by its electrical properties is almost certainly not going to work, as the electrical variation due to dirty contacts is much larger than that of a well-designed skimmer.
The attack you've shown relies on the card not being at all smart. Properly designed smart cards can still be dismantled for their keys, it's just much harder and more expensive: http://people.cs.uchicago.edu/~dinoj/smartcard/security.html