Yeah there's no justification for the branding either. Branding criminals so they'll be murdered in prison is about as anti Batman behavior as you can get.
I don't think he's branding them to intend to kill them by proxy.
He's marking them but as a repercussion in prison is maybe fellow inmates believe said branded criminal probably spilled beans to Batman's interrogation tactics. Thus other inmates killing them.
That's my theory, though like all the other dumb, half baked ideas in this terrible movie don't get fleshed out. Or retain any solid logic.
Let's get back to Affleck's performance. Which is ridiculously overrated on these fan boards merely because his character was more accurate in looks, though dramatically less in characterization compared to Nolan / Bale's Batman.
Affleck was boring, phoned in and bland. He let the suit and entirely modulated voice do all the work.

