Hey Cameraroll,
We'd be happy to help out. Unfortunately now that the libraries are merged, there's not an easy undo. To clarify though, are you saying that on both your Apple ID and her Apple ID, the same photos are shown? If so, as long as you're signed into separate Apple ID accounts at this point, you can each safely remove the photos you no longer want in your library.
Deleting a photo from your library would only delete from her library, if you're signed into the same Apple ID.
We'd suggest managing the photos from a computer or using iCloud.com though as you can more easily select multiple photos at a time for deletion, though you can still also manage from an iOS device as well if that's all you have available or just simply prefer.
Here are the steps using iCloud.com:
Delete photos and videos
1. In Photos on iCloud.com, select the photos or videos you want to delete, or double-click a single photo or video.
2. Click
, then click Delete.
3. Deleted photos and videos are moved to the Recently Deleted album.
4. To permanently delete photos or videos before they’re automatically deleted, go to the Recently Deleted album, select the items you want to delete, then click Delete [number] Items.
See also Delete photos or videos from your Shared Library.
This is outlined further here: Delete and recover photos and videos on iCloud.com - Apple Support
For help on iOS, check out: Delete photos on your iPhone or iPad - Apple Support
We hope this helps out.
Take care!