I am sure that your nanny knows your daughter well. If she asked for your daughter to be her flower girl, I am sure she is prepared for her to be herself that day.
I had my niece as my flower girl. She turned three a few weeks after my wedding. I knew she was young but wanted her to be able to participate. Our theory was if she walked down the aisle, great. If she stood nicely for pictures, great. If not, we understood. Our nephew was the ring bearer and he was a year older than our niece. We had them practice at the rehearsal and I gave my niece my practice bouquet from my shower and they both did great! The day of the wedding my niece made it halfway down the aisle and stopped and realized she couldn't find me, grandma or her dad and got a little nervous, but our nephew was great and stopped with her and waited for her to find grandma and helped her walk the rest of the way up the aisle. She ended up sitting on Grandma's lap during the whole ceremony rather than standing with us, but that was fine. She is in a few pictures and then got bored so she went and played while we finished up. Again, it was fine with us.
So what I am trying to say is that I am sure your nanny is prepared for your daught to act like a normal 2 year old. Whatever she does will be cute. I would suggest that you suggest to your nanny that your son and daughter walk up the aisle together and that possibly you or someone your children know very well sits on the aisle close to the front to be able to encourage them. Also, you may want to make sure your nanny is comfortable with your daughter sitting down during the ceremony if she doesn't want to stand up the whole time.
My one last suggestion would be for you to get a book about being a flower girl and ring bearer for your children and to practice for a couple months before the wedding. My Sister-In Law even found a video at the library for my nephew to watch and he was a pro by the time the wedding arrived. We gave a book to each of the kids and I think it helped them to know what was expected of them and to also get them excited about their important roles. There are quite a few books out there to choose from.
Good Luck,
D.