As the viewer, I saw him more as a symbol of the ridiculousness of their system, and the absurdity of zealotry. I only really felt bad for his parents. Even then, they were partly the architects of Thomas' destruction. On top of that, giving into the Nazis and becoming part of the system was indeed their best chance for prosperity, and even that lead to the early death of their child. So you have two parents who are realizing that the system is shit while being some of the most powerful members of such a system. John Smith became a shell of his former self with his movie obsession, halting all moral progress, and Helen actually made significant personal growth in that she saw the monster she became. Luckily the writers didn't need to beat you over the head with exposition to show you.

Give the viewer some more credit.