I think it will be fine. My oldest daughter's name is Gwendolyn but I always intended to call her Gwen. I love long names for when you are older but Gwen is better for littles I think.
I also call the other 2 by names that aren't their legal names and no confusion
I actually went to school with a guy whose legal name is Clayton but he went by Mac. I went to school with him k thru 12 and didn't even know his name wasn't Mac until 3rd grade when the teacher said Clayton. They have a place on school forms for preferred name and they even announced his name as Mac during graduation.
Anyways all that to say go for it
Though we have the courage to raise our daughters more like our sons, we've rarely had the courage to raise our sons like our daughters. -Gloria Steinem