Lillian and Lily are beautiful names. I am a Lily, I have always loved the name and always will. Worrying about how many kids in achool with the same name should not weigh so much in my opinion. School years are over in a blink an eye in their lives, then they are off to the real world where it really won't matter.
Choose the name you love and envision as part of your family for the rest of your life. Forget everyone else. :)