I... Think this ruling is good, even if you disagree with the Commons clause? I'm not sure I'm thrilled with limiting the speech of developers by saying they cannot ever place any restrictions whatsoever on how their code is used.
In my view, if developers want to add those restrictions, via the Commons Clause or otherwise, they should not license their work under the AGPLv3 (or other Open Source licenses). It appears the courts do not agree though, at least in this case.
It seems like the copyright holders assembled a chimera license that is in conflict with itself. The resulting ambiguity should be construed against the copyright holders and in favor of the users.