So you're all eating this crap up, aren't you?
Well, I'll say it then. Bullsh*t.
Apple is saying this because they don't make money on third party products, so they're going for the FUD angle to scare people away from buying things that don't pay them.
Folks, you're just fine using third party cables, you're no more likely to burn out your iPhone than if you use a cable made by Foxconn for Apple than if you buy one made by Foxconn for Joe Schoe's iPhone Parts.
Fortunately, the Lightning connector has a limited remaining lifespan anyway. The EU is about to kick Apple's butt for not using the standard Micro USB connector, and I'd seriously doubt Apple will produce an EU phone and a rest-of-world phone, so we'll see the benefits of EU law here. Conveniently enough, Micro USB is about the same size as Lightning, so Apple doesn't have to change the design much. Maybe we'll see it with the iPhone 6.