Yes, Applejack made Twilight cry. However, the whole basis of Winter Wrap up is to wrap up winter without magic. It's been the tradition of Ponyville ever since it was founded as a town and for Twilight to come in and use her magic just because she was feeling insecure and wanted to be part of it was really ignorant of Twilight to do, even if she had the best intentions. It's not much more different than if someone who celebrated Christmas tried to push their own traditions and stuff into Hanukkah just because they didn't feel like they fit in. And the reason she cried is not because she was yelled at, it was because she was caught and embarrassed.
It was already explained that Ponyville did do something to Trixie. When Twilight showed her up and got rid of the Ursa, Ponyville mocked and humiliated Trixie out of town. Not only that, but they spread the word of her failure so that everywhere she went, she was ridiculed and made a laughing stock. Had I been in Trixie's hooves, I would have done something similar.
If you think about it... it kind of makes sense for them to get upset at Twilight because she's not only acting like an overly possessive sister but she was also ruining a time in Cadence's life that is supposed to be perfect and happy. The other ponies didn't know she was anything but the real Cadence and they also hadn't seen her be rude or indifferent. When you're the only person who has witnessed something, it's going to be hard to convince people otherwise.
However, I don't believe they should have necessarily abandoned her, per se, but rather try to talk it out with her and maybe try to find the root of the problem. But it was convenient for the episode's sake so it had to happen, unfortunately XD