If you were to aid a 16-year-old runaway but contacted social services for help while you had the minor sheltered could you still be charged for aiding or harboring a runaway child?

You should have contacted the police when the teen came to you for help. If that child is reported missing, you could be charged for kidnapping.
There must be a good reason for the child to be running away, and that is up to the police and social services to decide, not you. I know you were just trying to help, but if the parents want the child back, it's out of your hands.
If they don't care about the child, they could sign over gaurdianship to you. Whatever the case, the child is lucky to have you and I hope it all works out.