Yes, you'll want to use a different email account for iMessages on her iPad. You can leave your's if you want, and add a new one (provided she has her own email address); then just remember to use that email when trying to call her.
Just tap Receive At in Settings > Messages, then Add Another Email. If I remember my GMail accounts worked fine, but my Yahoo one didn't. Once you've set up the new email account it should be possible to remove yours if desired. Just tap on it and choose Remove This Email.
There is no need to sign out of your Apple ID, unless you want to give her an iCloud account of her own, and use that email address.
You can set up FaceTime the same way, btw.