Microsoft's contention was that using GPL'ed software exposes you and your intellectual property to risk. The motivation of the parties making very broad GPL claims is not relevant - what's relevant is that it is precisely the sort of thing Microsoft was insinuating and precisely the sort of thing the linked missive tries to disclaim.
Joe Nobody, author of Yet Another PHP Blog Engine
Matt Mullenweg is hardly Joe Nobdy, nor is Wordpress Yet Another PHP Blog Engine. He represents his claims as legally sound and offers the opinion of lawyers who are, according to him "the world’s preëminent experts on the GPL". See:
http://wordpress.org/development/2009/07/themes-are-gpl-too/