How do the events of "A Wrinkle in Time" teach Meg and Calvin the positive side of being different?
Meg and Calvin learn throughout the story that when they are weak, then they are strong. It is exactly those points that they are "different" that enable to overcome IT and the power of evil.
For example, Meg's impatience turns to perseverance in the rescue of her father and Charles Wallace. Her math abilities, while they may make her an "odd ball" at school, enable her to concentrate her mind in resisting IT.
In contrast, Charles Wallace tries to use his strength to overcome IT, and ends up within IT's grasp. His pride (or hubris) led to his downfall, while Meg's and Calvin's humility protected them from submitting to something they didn't quite understand, but knew it was evil.
Moreover, Meg's strog sense of love (which could be seen as carried to the extreme as a point of weakness) enabled her to pierce IT's power over Charles Wallace and rescue him.
The overall message is that in the ways we are different, we become best suited to whatever task is set before us.