I wouldn't say it is quite as bad as he is saying, but it is a possibility. Given the complex nature of the human microbiome I think he doesn't fully understand how hard it is to shift the microbiome that way. There is a reason a lot of our best antibiotics (vancomycin etc.) come from bacteria...they are waging war on each other every day in the soil, in our bodies, on our bodies...everywhere.
We barely even know how to study the microbiome, let alone decide a single bacteria can cause an entire disease, evade the immune system, and evade the entirety of our microbiome which more likely than not has bacteria in it that can fight off that strain. For all we know the susceptibility he is talking about is our lack of a strain of bacteria (or bacteria that have inherited the right gene cluster) that can fight off a MAP infection without intervention. That could easily explain how some people get crohns and others dont and why antibiotics can sometimes be "the trigger". But until we have cataloged thousands of microbiomes (and keep in mind he was correct about the difficulty of culturing a number of these bacteria), we will be unable to definitely say MAP or any other bacteria is able to cause a disease like crohns.
I do like the article though and think it brings up some interesting points that hopefully scientists (like Michael Fischbach at UCSF) can use to answer some lingering questions about crohns and maybe bring us a step closer to a cure (for some people at the very least)