You need a Mac to compile (unless you're into serious jailbreak mojo -- which Apple is not) with Apple's internal IDE and tool creation suite. You need a Mac to create professional graphics and video suites. You need a Mac for high-end publishing and so forth. So all of us agree: The Mac lives and OS X for the desktop is not imperiled.
But I agree with Lyons' actual point, that desktop computing is taking a new and unexpected backseat to a consumer-oriented series of devices. Lyons writes, "[Apple] will keep pumping up the capabilities of iOS 4 so that iPads and other future mobile devices can displace the Mac." I would have changed that last period to a comma and added, "for a very large new audience of Apple consumers."
Don't be so tied to your conservative notions about what a computer must be that you aren't willing to think forward. Devices must serve the consumer, but beyond that, the gates are newly open. Computers today don't look like the desktop systems that we've been using for the last 20 years. My iPhone is a flexible OS X-powered system, offering excellent support of many of the computing tasks that most people use. For some reason, these tasks are too-often dismissed when described as "light computing" and yet, they describe the computing that a huge number of people do. They check e-mail, they surf the web, they play games.
Apple's well-priced, beautifully designed, and insanely portable systems have hit a consumer sweet spot. People love them, and are buying them in droves. Apple's customer base has exploded. The iPad in particular does what many home users want a computer to do, and the truth is that the majority of computer users are those home users. Apple would be foolish to ignore that huge customer base.
Importantly, that base isn't demanding Macintoshes. They do want an Apple product, but the product they want is not desktop OS X. It's iPods, iPads and iPhones. And when they dock those products to their home computer, it's often a Windows system that is running iTunes, not a Mac. The demographics have spoken.
So is the Mac going away? No, it's not. Has the Mac been relegated to the steaming dung heap of the past? No. And notice that I didn't quote that steaming dung heap bit? That's because the letter that got sent to Steve Jobs last night, to which he replied "Completely wrong. Just wait", used that bit completely out of context. Lyons was talking about Mac enthusiasts, not the Macintosh itself.
He was talking about the Mac-only fanbase. He was saying, that the "future of Apple is no longer centered around the Macintosh." And he's right. It's not. Mac isn't dead, but Apple is smart enough to know what sells and where the future lies. Consumer devices, not general computing, is where Apple has been making its mark in the world and will continue to move forward.
So what do I think about Jobs' reply? I think that it adds no new information to the discussion. It answers the wrong question. The question isn't "Is Mac dead?" The right question is "Where is the Mac heading and how must it evolve to get there?"
 I choose to ignore the actual title of Lyons' piece. It's too much cognitive dissonance.