User blog comment:Druidinhiding/Alternate Ending Theories and Thoughts/@comment-5102537-20121227220234

That's an interesting theory. Alas, I think that the reason was much more ordinary and simple one. Maybe they had other plans at that point of time, but since there were those comments from the official side that villains shouldn't be made likable, in regard to Uther, who wasn't even a villain and who they made evil all of a sudden, as we know, they probably didn't want to make especially Morgana  likable either. Giving the insane evil villainess redemption but claiming that Uther was a villain and must not be likable would make no sense. So it was much easier to simply get rid of both the way they did.

Moreover, if there was even the slightest possibility of an alternative ending and that this one happened because Arthur made the "wrong" decision, there would have been a hint. In case they really intended to show it the way you described, they did (again) a very bad job on it. To make the audience think about such things, hints are needed, maybe a mentioning by someone (character) or something like this. Without even that, it's all only a riddle without an answer. That's not what stories or TV shows are for, especially not a shallow one like "Merlin". I think it's somewhat mean to leave the fans without even slight explanations and possibilities while they are trying to find solutions for all the plotholes and unanswered questions.