That's partly because Peter Bright (the story author) overstates Microsoft's case. SDP is a problematic part of the current spec, but most of those problems are just things that it can't do yet, and if you look at the mailing list thread responses to the messages he links to, you can see most of the discussion is about moving SDP expansion discussions back to the IETF working group. This will slow things down, but that's how standards work sometimes.
But, SDP is only a part of the spec. Meanwhile, Microsoft's proposal retains essentially none of the current WebRTC spec. That was the real issue with their proposal, coming relatively late in the game, and why it's misleading to put the disagreement in terms of only SDP. Microsoft's reps have issues with how the connections are bootstrapped, but took the opportunity to rewrite everything else while they were at it. That's certainly their prerogative, and is again how standards are sometimes produced, but the issue is more complicated than "SDP is bad, but the W3C is clinging to it" as Peter tells the tale.
I agree that Microsoft is moving in good faith, however. As a good parallel, see Firefox's incompatible Audio Data API, produced just as the Webkit-born Web Audio API was picking up steam. When specs are early and still being worked on, sometimes the best thing is to produce a working implementation, to show others that your proposal really is as good as you say it is. That isn't necessarily undermining the standards process, nor is it a sign of the process not working. It can be, but at this stage, Microsoft is still engaged, even if they are just repeating why they think their proposal is better.
It will slow things down, but standards work is sometimes really slow, especially when people disagree, and growing pains are inevitable. You can only hope this gets sorted out fast enough that the spec is still relevant by the time it comes out.