Here's a weird admission. Up until recently, the most effective and difficult moral choice I've ever had to make in a game was in Fable III. At the beginning, the king offers you a choice of who to kill; some villagers or your childhood sweetheart. If you take too long, the king suddenly starts counting down from ten, at which point he will have both parties executed.
It's almost the perfect example of what a moral choice can be. Often in games, when presented with moral choices, we play tactically. We don't go with our gut, we try and "game" the system and play tactically. The moral decisions in BioShock, for example, aren't really about ethics, they're about whether or not you want upgrades now or later.
Sticking the time limit on a moral choice that doesn't immediately offer any advantages either way is a fantastic way of giving a moral choice weight. It worked in that first bit of Fable III and by god does it work in The Walking Dead game.