You just haven't found the right MBA :)
Some quick background: I'm attending school part-time for my MBA (Richard Ivey, case-based). I've also been with a successful YC startup from the the ground floor as a technical hire, and am currently the co-founder of a very early stage startup.
Your article raises some really good points - most of which I agree with completely. Execution is key, and becoming a PM at an early stage startup is misguided if you're not able to implement your ideas.
That said, should a startup outright ignore applicants with MBAs? Like most things...it depends. The leadership, communication and (yes) strategic skills that a good MBA provides are important. Coupling these strengths with a technical background is a pretty powerful combination.