Could be so, but it would just be weird that he could still post K and BB rates like this if strike throwing was his main issue. I guess you could rationalize it somewhat like this:
He has a lot of trouble throwing that slider for a strike. It's always finishing down and out of the zone.
This is leading to a small spike in BB rate, but also an increase in the K rate since it's acting very much like an out pitch.
However, for players that can recognize the breaking ball, they can essentially forget about it and sit fastball. This explains some of the "hittability" (BABIP and HR/FB), and by extension, some of the grossly high ERA.
.... But then we're just constructing stories, probably.
It's only 81 innings though, so I'm comfortable with just hanging the weird numbers on the small sample size hook and moving on. For me, JJ will go into 2014 not much worse than he came into 2013 - as a huge injury risk with some upside.