I think you articulated my biggest complaint with this episode better than I could have.
I know some people can be very vocal about their opinions regarding the show (I've expressed on more than one occasion my dislike for the characterization and plot in "Princess Spike" for instance). And I think there are good rebuttals to common criticisms of the show- the Fluttershy one is a good example. People criticize her for often falling back to her shy, unassertive self, or her lack of consistency, but, as she pointed out, can anyone really say that they immediately started behaving better after learning a lesson and never lapsed back to their former tendencies? There are some lessons in life you have to go through more than once.
So do I think it's important to keep in mind that these ponies aren't perfect and address these complaints? Of course. That doesn't change the fact, however, that these are still legitimate complaints to be made against characters. I don't think I can really fault people for not liking Rarity because they think she's shallow (heck, pre-season 4, that's what I thought about her, even though I didn't really dislike her or anything), or pointing out that they don't like Fluttershy because she too often goes back to being a doormat. As long as those assertions are reasonable and grounded in at least some evidence, and the critics pointing out such things are not being overly rude, they have a right to think what they do. However, the biggest problem with the ep was that it seemed to be saying "Those people are a**holes".
And I think it's because of what you pointed out- that making the analogy between fans harshly (but perhaps fairly) criticizing a show and its characters, and townsponies trashing their fellow ponies, kinda fell flat. They're not really the same situation. I feel like that comparison kinda would hurt the case for the lesson they were probably intending to go for.
That criticism aside, I feel like Toola Roola and Coconut Cream being brought in at the end gave the ep a more nuanced moral however, rather than just "Yeah, we know we're not perfect, now shut up about it." My favorite way of interpreting this episode is that it's kind of a lesson to both the mane characters and the fans- kind of like a lesson for the show staff and the pony fans:
1. The characters we know and love aren't perfect, and that's what exactly what makes their stories so interesting and special.
2. There will always be people who criticize you or the things you do, and that's fine. You may not be able to change their opinion of you, but you can change how you let those opinions affect you.
3. If your story genuinely inspires even one person (or group of people) to be better people, that's where the real reward is.