Kryptonite is the Deux Ex Machina of the Superman universe. It's super rare, but all of his villians seem to get ahold of it.
It just makes sense that this would transfer to the Smallville universe.
At least it wasn't some Kryptonite infused lie detector like the write up made us believe. The show has set a precedense that Kryptonite is used in Jewelry making ala Whisper and Red, and at least him being a Jewler made more sense that a bracelet he is wearing could have Kryptonite as it's stone. They needed an excuse to make sure Clark was weakened for a bit, so it wasn't a super easy bust and grab for Clark.
Plus it resulted in some great stuff, like Clark headbutting the guy and very smartly using the drainage grate to get rid of the bracelet.
Stuff like this is just something you have to accept when it comes to Superman related media.