Apologies, but I disagree with basically everything you're saying here.
Branding isn't hard; forcing a constructed brand is hard. That's the real source of friction here.
A brand might be way more than a logo, but THIS brand is not. That logo is literally the only thing this design agency contributed at all. Even the colors were already in use around the project. If the difference between "a brand" and "a logo" is "ten pages of marketspeak" then I'm even less convinced that branding is hard.
I read the "brand guide." It's exactly what I expect from a professional design firm: meaningless noise, carefully typeset. The entirety of section 1 is a PR quickref chart, of no interest or use to anyone but project managers dealing with micromanaging executives. Section 2.0 is breathless pseudo-art crap and some trademark defense. 2.1 contains pointless backstory for fonts that are firmly in the "Google already had lying around" category. Finally, the cartoon gets its own section, expressly to head off the whining from the old guard.
I've also seen a ton of this crap over the years, and none of it has ever made the slightest bit of difference. This is exactly the kind of time-and-money-wasting that occurs when some facet of management has gone off the rails. Let's hope the derelict in question is somewhere in marketing, and unable to affect the quality of the actual technology in question.
As for the actual logo, I don't have an opinion about it. I don't think there's anything there to have an opinion about. I've never been a big fan of the gopher cartoon, but at least it had some character, which likely comes from the talent of a real artist.