The only thing that makes sense about keeping Pena is that if he walks at the end of the year the Cubs get a pretty high compensation pick for losing him.
Not necessarily. Pena was so bad in 2010 that he's on the border of earning the Cubs a pick. At best, he'd be a Type B free agent, which would get the Cubs a sandwich pick, not a first-rounder.
I'm sure a sandwich pick was enough to sell Hendry on keeping Pena.