Phone your surgery now and ask for your daughter to be examined by a different doctor with a view to a referral to a gynaecologist.
There are many causes of an inflamed and hard clitoris, mostly they can be dealt with by either internal or external antibiotics, but rarely the problem is something else altogether that does not respond to antibiotics.
The doctor cannot be certain that the cyst is completely drained, or even that the two problems are related.
Constant pain in that area is not normal and it needs proper attention.
This link has lots of information about problems in that area in pre teens, most will not apply to your daughter but it does demonstrate the many different causes of your daughter's symptoms.
http://books.google.co.uk/books?id=y46Ze-7WXY8 C&pg=PA111&lpg=PA111&dq=clitoral+cyst+in+9+yea r+old&source=web&ots=p2hGVJAWl4&sig=bYGcOkSoV_ l7oYcLk3xcuniwedg&hl=en&sa=X&oi=book_result&re snum=10&ct=result#PPA109,M1
Please do not be alarmed by the content, I just hope it persuades you that an examination is absolutely necessary