You've interpreted the data in the most positive way possible. Yes, that is one of many ways in which things could have unfolded.
But as the article says, this is all secret. We don't know what exactly Google and the NSA built together in that first agreement shortly after the Chinese hacking scandal. And we don't know what else has happened since then.
Maybe it's all innocuous stuff, as you said. Maybe it isn't. To just assume it is all good or all bad seems unjustified by the amount of actual facts that are public.
But as the article says, this is all secret. We don't know what exactly Google and the NSA built together in that first agreement shortly after the Chinese hacking scandal. And we don't know what else has happened since then.
Maybe it's all innocuous stuff, as you said. Maybe it isn't. To just assume it is all good or all bad seems unjustified by the amount of actual facts that are public.