No, I think you got the origin of the term right, where the girl is, on average, shorter than the guy. Although it probably wouldn't hurt to look it up on
Urban Dictionary, they might have something on there.
I have a harder time figuring out how "boyfriend/girlfriend" got turned into "boo".
EDIT: "boo is a term that is derived from the French word "beau" meaning beautiful. In 18th century England it meant an admirer, usually male. It made it's way into Afro-Caribean language perhaps through the French colonisation of some Caribean islands.
Now meaning girl or boyfriend"
Sounds reasonable.