Kristen,
Do you have a screen door? If so, can you take it off and put it in front of the door Lily is in? That way, they wouldn't cry or scratch and they'd still be separated?
Integrating a new cat can be very stressful, its hard dealing with scratching on the door when you just want them to go lay down and be happy. :) Just be patient and they'll come around.
As far as Luna, make sure she's given a TON of extra love. That way, she'll have a hard time being mad at you. ;)