The certification of Linux means that MS has gotten exactly what they wanted
It's too bad geeks aren't strategists, because if they were, they'd understand that MS has just employed a classic tactic, called the Defense Through Subtle Distinction, where you call attention to any ambiguity in an opponent's proposition - no matter how small or 'subtle'. Then you can exploit it, by creating a distinction - pointing out how you (or your products, services, etc) are superior. This is a chink in the armor that can be widened with a huge variety of other tactics.
Look, the truth does come out in the end - even in nasty places like markets. The point is that it can take a long time - and you might not be around to see it, unless you can think at least a little strategically.
Of course, this decision will have huge knock-on effects on the innovation rate of the user base and, most importantly, the incentive to innovate, because it shifts the gains to innovation.
Bad move - really bad.