Besides the bias question (which is possible and apparently likely for both sides), I realize this is a touchy subject for many but the tone of this article is rather more irritated than it really needs to be. They even mention that the authors of the Harvard paper said the study wasn't meant to show causality, but the very next section heading is "Ridiculous things you can 'prove' caused cancer mortality," which suggests that is what the authors of the original paper were trying to do. If you're going to accuse them of being deceptive, at least be open about it instead of using this sort of passive-aggressive approach.

Also, they say:

"Over the last several months, we have replicated the results of these papers. The authors supplied us with eight lines of code and answered a couple of questions about the covariates, which did not replicate the results. Most of our replication was done through first principles combined with trial and error. Once we were reasonably close to the results of the first national study on cancer mortality, we took the methodology and applied it to numerous other landmarks."

I'm no expert in experiment design, but unless I missed something, I have qualms about calling this method a true "replication."