Aren't you argueing against your own first statement? If some people like to eliminate some canon factors they dislike in their own creation, isn't that their right as a creator?
Also, I doubt anyone here would argue that they don't have the right to do this. It's the same thing as with the Mass Effect 3 ending. The majority of the community, or at least a non-negliable part, really disliked it, but the creators didn't change it.
I even doubt that they dislike Alicorn Twilight or the episode. It's just that this would have been a great ending for a later season... not this early.
Further...
What I hated most about the episode is that it consisted of 8-10 minutes actual plot, with the swapped cutie marks, the "conflict" of the episode and then the other 12-14 minutes of the episode was just about Twilight and her becoming a princess and an alicorn.
I think the 12-14 minutes for her transformation were necessary, but they shouldn't have cut that time off of the plot, "solving the conflict", which is the most interesting and fun part of a show, a book, a game. It really should have been a special episode with twice the length or two parts like the endings of the last seasons.
That it was too early to dish out this kind of "ending" is personal opinion. The other thing I mentioned is just bad dramaturgy.