I paid him back because he's one of the few characters I actually like. I did it early when 21k was actually a lot of money to, which felt very rewarding to me. That feeling is all the reward you get though. As far as I can tell (and everyone else seems to agree), there is no tangible reward for paying back the debt. I'm okay with that honestly. If we got rewarded for it doing the right thing, then it wouldn't feel like we were doing it for principle. IMO, a game should reward greedy actions with money and gear. A game should reward altruistic actions with NPC behavior and dialog...and maybe over time a reputation that offers an advantage in some situation. We didn't get that last part here, but it still felt good paying back Vik, so I'm happy with it.
On the mechanics side we totally got ripped off. You can get a Mk 3 version of the eyes installed for a mere 5k.