I admit that you have a strange naming tradition, but Pomegranate isn't the strangest name that I've ever heard and at least you can call her
Meg. I don't really care for the way Pomegranate sounds though.
Other ideas:
Tangerine nn
Angie or Tangie
ClementineCherryCerise (means "cherry" in French)
Blossom - Related to fruit trees.
Sakura - Means "cherry blossom".
Tresnja - "cherry"
Mei - "plum"
Li - "plum"
Pear (nickname
Perry)
Ume - "plum blossom"
Umeko - "plum blossom child"
Prunella nn
Nell,
Nelle,
Nellie,
Nella,
Ella,
Ellie, or
Elle - "plum"
Avalon - "apple"
Cam - "orange"; this is probably referring to the color though.
Berry
This link might be able to help you to come up with more ideas:
http://www.crfg.org/pubs/fl/commonAC.html
I don't recommend using Apple though. It's too celeb trendy for me.