Daniel to say the least has seen the horror of prison. Indeed, the episodes this year, especially the first, have gone out of their way to show how soul-crushing Daniel's time on death row was. Could Daniel's refusal to implicate Bobby Dean derive from Daniel's unwillingness to be responsible for sending any other man to prison, even one who nearly savagely killed him? Perhaps.
Let's look at the other end of the continuum. When Amantha screams at Daniel about how could he just let Bobby Dean go with no retribution, Daniel mutters something to the effect that that's not necessarily the case. What was Daniel alluding to? That he would punish Bobby Dean with his own hands? Also, perhaps. Or, could Daniel have been thinking that Bobby Dean will pay the price of living with the memory of his nearly killing someone, as maybe Daniel feels about his beating of Teddy, or maybe about something much worse?
Or, might Daniel have a completely different motive for keeping Bobby Dean out of jail? If this were more of a high-puzzle murder mystery than a scathing and tender examination of the human psyche - Rectify of course is both, but it's more of the latter - than perhaps Daniel might want to keep Bobby Dean out of prison, as a way of ultimately proving that someone other than Daniel - maybe Bobby Dean? - was the murderer.
And then there's the other, worst side of this. If there's any chance at all that Daniel indeed was responsible for killing Hanna, then he would not want to punish someone who was beating him for good reason. It's almost impossible to believe that someone with Daniel's gentleness could hurt anyone. But we did see him beat Teddy last season, and it's a measure of how superb this drama is that we can eve contemplate that question.
See also Rectify 2.1: Indelible ... Rectify 2.2: True Real Time
And see also Rectify: Sheer and Shattering Poetry ... Rectify 1.5: Balloon Man ... Rectify Season 1 Finale: Searingly Anti-Climactic
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