If you are a gaijin girl who is tall, I don't think you need to worry about people not liking you in Japan. Many Japanese guys will probably want to talk to you even more!
Also, 5' 9" is not really that tall. If you are in rural Japan, the older Japanese people may still be shorter, but in central Tokyo many of the young Japanese guys and girls are quite tall. Even when the Japanese girls aren't tall, some of them wear 5" high heels.
Take a walk around Shibuya and you might be suprised by how tall some of the Japanese people are. Everyone is used to foreigners in Tokyo too, so I doubt anyone other than small children would be shocked by tall foreigners.