Well, then I guess saying "Hello my little munchkin" wouldn't be a good idea, huh? LOL
Just be honest, and tell her you have NO IDEA why you said what you said. It just came out, and you can't even justify it. Tell her you LOVE her just the way she is, and you always have! Tell her you wouldn't want her any differently -- you CHOSE her because of the way she is. You didn't CHOOSE any tall woman -- you chose HER. And you don't WANT anyone else!
You may have to keep boosting her self-esteem for awhile until she forgets that remark -- hopefully she will (until she sees another TALL woman. LOL). Just try not to look at tall women.

At least not when SHE'S around.
I hope things will be ok. Perhaps take her a little gift when you go home. That might help. God bless & good luck. Hugs, Lee