I personally think that the writers want to forget that particular episode of KH saga, and because of that they aren't interested in making Sora remember. It is one of the most dark and mature ones, and is the only entry in which the original Organization looks truly evil and dangerous, committing to almost sadistic crimes.
If now Lea is a full light hero, Ienzo was just an innocent orphan who doesn't understand what was going on, Lauriam is just a concerned brother, and Elrena was just doing everything for love (perhaps exaggerating a little, but still)... they just can't have the main hero Sora undertaking a moral crisis trying to understand, justify or forgive all Axel, Zexion, Marluxia and Larxene actions.
Of course, I think that they will help the narrative growth if they address this topics in-game, whether it is to go to a believable redemption arc or just to create internal conflict and doubts on Sora and help him mature up. Naminé issue, as has been said, is so flagrant that I even prefer no to mention it.