Well, as your girlfriend, many uncircumsized guys have extra foreskin, or maybe their penis is leaning towards a side, or even maybe it is too little or too big! Human body is not perfect, and will never be. What I am trying to say is that if she feels uncomfortable with it, try make her go to her doctor and ask him if they can remove that piece of extra skin? It should not be a complicated surgical procedure, and well, she will be more confident afterwards.
In the meantime, you can tell her that you love her the way it is and if she needs more time to get used to her body the way it is, you can only be there to support her. At the end you love HER, not her vagina
Good luck to the both of you.
-Jean