I am honestly stunned nobody figured out, but then again, I do have enough knowledge to mindrape most people with what for me is basic knowledge.
The school is a parallel to Equestria, the two keep each other in balance, that is why Celestia wouldn't send the others along, and also didn't destroy the portal. If the others would've gone in, it would most likely give major time/space issues. If the portal would be smashed, it would be like drawing a line through Yin and Yang. Also, Sunset Shimmer's cutie mark is a sun Yin/Yang, and she doesn't have a human counterpart, as the only one (seeing as Twilight has one in another city). Coincidence? I don't think so... Also, she adapted fairly well, and managed to keep anyone from finding out she just appeared some time ago, and "doesn't have parents". Quantum leap rules may have applied to her, because she could actually have to do with more than two worlds.
Anyways, smashing the portal would entirely disable the balance keeping of the two, since they are no longer connected. It is like having a door that can open sometimes, allowing for occasional connection, and replacing it with a wall, completely disabling it. The lack of balancing would result in the "magical" (actually, it's just psionic energy) connection between the two being thrown out of whack, disabling all forms of magic.
Pegasi wouldn't be able to control weather, fly with those small wings, or walk on clouds. Unicorns wouldn't be able to use their magic. Earth ponies would lose strength and crop growing abilities, ponies wouldn't be able to hold stuff as well anymore (general pony magic), friendships would also become more fragile, the Elements would be disabled, as well as the Crystal Heart and all magical creatures, and most likely the entire Equestrian society would collapse. Earth would survive because they don't have magic anyways, and that lack of magic is what is keeping the balance between the two, and that is the "magical" connection. Really, it is just the other side of the "Yin/Yang." The only way Earth wouldn't survive is if the whack of balance was strong enough to rip time/space apart, leading to complete destruction of both universes, but that seems unlikely.