You need to migrate her device to a different account. To do this, start by saving any photo stream photos that you want to keep to your camera roll (unless already there) by opening your my photo stream album, tapping Select, tapping the photos, tap the share icon (box with upward facing arrow), then tapping Save to Camera Roll. If you are syncing notes with iCloud that you want to keep, you'll need to open each of your notes and email them to yourself so you can later copy and paste the text into new notes created in your new account. Then go to Settings>iCloud, tap Delete Account (which only deletes it from this device, not from iCloud; your devices won't be effected by this), provide the password to turn off Find My iDevice and choose Keep on My iDevice when prompted. Then sign back in with a different Apple ID to create your new account and choose Merge to upload your data.
Once you are on separate accounts, you can each go to icloud.com and delete the other person's data from your account.
Note: you can continue to share the same ID for other services such as iTunes if you prefer. The ID does not need to be the same as your iCloud ID.
Also, you should avoid using the same ID for iMessage and FaceTime or you will end up getting each other's text messages and FaceTime calls. If she is, go to Settings>Messages>Send & Receive, tap the ID, sign out, then sign back in with her new iCloud ID. Then do the same thing in Settings>FaceTime.