Not really. Thesis shouldn't be considered a derivative work. If it is, than any application that runs under Linux should also be considered a derivative work (you need Linux to run the app..right?).
Should any app compiled using GCC be considered derivative work?
"The permission you need—to convey the object code from these GCC libraries under your own project's license—is primarily contained in section 2:
You have permission to propagate a work of Target Code formed by combining the Runtime Library with Independent Modules, even if such propagation would otherwise violate the terms of GPLv3, provided that all Target Code was generated by Eligible Compilation Processes. You may then convey such a combination under terms of your choice, consistent with the licensing of the Independent Modules."
I don't see how they can automatically assume that all themes are under the GPL license. If you make a theme that does not use any existing wordpress code, it wouldn't be considered a derivative work.
"The PHP elements, taken together, are clearly derivative of WordPress code.... They are derivative of WordPress because every part of them is determined by the content of the WordPress functions they call. As works of authorship, they are designed only to be combined with WordPress into a larger work."
I personally would consider that to be impossible, however, you are basically correct.
In this specific case though, that does not apply. Thesis makes heavy use of WordPress code.