Obviously, Google could be lying in their most recent denial that disputes such a claim. They are, after all, required to lie if they are directly and materially involved in the program.
On the other hand, were I the business owner of a corporation that held millions of people's information and the NSA approached me for access, I don't think it is at all inconceivable and unlikely that I would attempt to negotiate not having the NSA on my network, in my machines, so I could retain the ability to truthfully tell my users that the company did not allow direct access to company servers.
In the article, Mr. Horowitz suggests that, given other leaks and information we've had in the prior years regarding NSA tapping the internet, the slurping of company data is happening at the on/off ramps to the networks, where data is coming in/out. This is far more likely than Google shipping off deltas in cron batches. Thus, Google et al. can appear on the PRISM Powerpoint, which just says their data was added to the system. That can mean anything, you know. The Powerpoint presentation is hardly a source of empirical data presenting the technical architecture of the program.
This article is attempting to help educate and achieve protection at all hops, not just the hops between you and Google. Perfect Forward Secrecy is just for that purpose--it removes the ability to find your encrypted data crackable via single master key decryption by using temporary keys.
So, while Google can only do so much in resisting NSLs, perhaps there is a little bit worth appreciating here. Google can't stop the NSA from slurping up traffic. But they can prevent that data from being massively decrypted via a single key.