Why is Mrs. Who's quote in chapter 12 relevant to Meg and IT or to good and evil?
The quotation that Mrs. Who gives to Margaret in chapter 12 is 1 Corinthians 1:25-28:
Because the foolishness of God is wiser than men; and the weakness of God is stronger than men. For ye see your calling, brethren, how that not many wise men after the flesh, not many mighty, not many noble, are called: But God hath chosen the foolish things of the world to confound the wise; and God hath chosen the weak things of the world to confound the things which are mighty; And base things of the world, and things which are despised, hath God chosen, yea, and things which are not, to bring to nought things that are.
This "gift" makes sense when it is combined with the gift that Mrs. Whatsit gives Margaret: something that she has that IT does not. That thing is love, which is foolish and confounding to IT (to confound means to frustrate). The "weakness of God" is the ability to forget yourself and love the other person, which is how Margaret defeats IT and rescues Charles Wallace.