Okay, I think I've pinpointed exactly what it is that bothers me. Exactly why Ponyville's prank feels so much worse.
Compare it to the prank Dash pulled on Fluttershy. Sure, she really scared Fluttershy, but then she pulled the mask off and it was over. At the time Fluttershy thought she had run into a scary creature, but that was it. I felt really bad for Flutters here, and Dash continuing to laugh at her is pretty insensitive, yeah.
Then comes Ponyville's big prank, and it's a similar scary one, but taken to the extreme. It's not just one monster, it's a lot of them. It's not just a random dragon thing, it's her best friends, and the whole town. It's not a random event, it's HER fault. As far as Dash know during the prank, she's caused serious harm to everypony she knows, and now they might be about to hurt her. She's not just feeling scared, she's probably feeling horrible guilt.
It doesn't end quick either. It get's dragged on and on. Dash went too far, but her friends pushed it even further, too much in my opinion. Heck, I can imagine the whole scenario scaring Dash off from ever pulling a prank again, not just cause she doesn't want to be mean, but out of a huge fear of hurting anypony.
Actually, that could make an interesting episode. Dash taking the lesson to heart so much she becomes overly sensitive around her friends, to the point of not acting like herself at all.