Will deleting Clash of Clans on an old device affect progression on a new device?
You can delete Clash of Clans from the old phone and it won't affect Clash of Clans on the new phone.
You should create your own Game Center ID to play on the old phone. This will ensure your games don't interfere with her games. See http://support.apple.com/kb/ht4314 for steps to create a Game Center account if you don't know how to do this.