You bring up several ways the patent system isn't right, but it isn't clear that any of it amounts to extortion.
In your last paragraph, you hint that the barbecuer doesn't legally owe the royalties -- that if he paid for legal process, he wouldn't have to pay the royalties. If that's true, and Kraft knows it, then we have extortion. Kraft has a moral (and often legal!) obligation to leave him alone for free, but is offering to sell it. This has nothing to do with patents; this kind of extortion exists throughout the legal system.
But if Kraft really has a case, you have to dig deeper to find any extortion. You have to base it on a personal belief (which many don't share) that a person can't morally own an invention of this type. Much like many people believe one can't morally own, in one way or another, a person, a body part, or land.
With respect to some of the other problems you brought up: I am not a patent lawyer; most of what I know about patents comes from places like LWN reader comments. But I can tell you this:
US patent law requires an invention to be nonobvious to have patent protection. The US patent office seems to be largely ignoring that rule these days, but courts have been sticking to it better. If you can invent something by "applying common sense to [your] profession," it's legally "obvious."
The fact that independent invention doesn't excuse you from patent liability (i.e. if I invent something without knowing that you already did, I still can't use the invention) is based on the original purpose of patents referred to in an earlier comment: The patent protection is compensation for contributing an invention to the public (within limits). It's not a recognition of a moral right of an inventor to his ideas. The guy who gave the mouse invention to the public did his part; as a member of the public, your part is to pay him when you use it, regardless of whether you had the same idea.
I believe with the current state of technology, the public is getting a bad deal on most patents -- it's paying for inventions that would have been contributed anyway, because there would be no way to keep it secret and it cost practically nothing to invent.
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