Actually, I dont think you did much wrong. Saying you would love her taller is just a throwaway comment, you meant no harm. Its not like you said you wished she had a smaller backside or something is it? She cant help her height but she can help not take everything personally.

I do think she needs to work on some of her self esteem, and not have you walk on eggshells. If she broke up with you over this, then it would'nt be your fault, it's too trivial. You should hear some of the stuff my partner and I say to each other! But we laugh it off, knowing that underneath any teasing or throwaway comment, we love and care for each other.

I agree with Leed, she should take comfort in that she and you are together, and you love & want to be with her, no matter what her height is. And then leave it at that. Its up to her what she does with it.