Spoiler Alert! I noticed something I hadn't caught before. When Flynn recounts Tron's valiant defense of him during CLU's coup, Tron's disk is shown as being infected with the orange light of CLU's cause. Later, when Quorra offers herself as a distraction so Kevin and Sam Flynn can get away, Tron's orange disk is then shown as being re-infected with her 'good' blue light. I think that's part of why he decides to defend the Flynns from CLU during the air battle.