They do have a valid point about protecting their customers from poor quality counterfeits. There's a story going round in cycling world this week about Specialized pulling up a bike shop called Cafe Roubaix, Roubaix being a name used by Specialized. One of the issues Specialized has had to deal with was when they had a bike returned after it snapped causing significant injuries to the rider, only to find that the bike itself was a counterfeit. Since then they've paid a law firm to track down counterfeiters - the Cafe Roubaix owner got caught up in the cross fire a bit. As long as Canon continues to allow you to use a 3rd party battery, after clicking 'OK' to continue I'm fine with it. They're warning you that your camera might get fried - but leaving it up to you to make the decision. I still use a 3rd party battery as a spare, but use the original Canon as my primary battery.
There’s a big difference between third party components that are labeled as such, and plain out selling counterfeit wares. Especially when your counterfeit is replacing an expensive process like carbon fiber manufacturing with a cheaper and inferior process, and when that has safety concerns. Lithium Ion battery technology isn’t exactly rocket science, Canon just puts an over-inflated premium on theirs to milk some more money out of consumers. Third party component manufacturing is a legitimate business model and helps keep manufactures honest (less dis-honest?). If the quality of the product manufacturers components truly are better, or the price is marginally more, people will buy them because it gives us a warm fuzzy feeling to see that name brand printed on the side. You only need these kind of tactics when you’re trying to force people to buy your overpriced product.