Here is what I believe to be true. When you enable iCloud Photos, the system will attempt to detect and avoid duplicates based on photo metadata. So if the photos on the iPhone and the Mac are indeed the same (as in, they were synced via USB through Photos.app), then iCloud is usually smart enough to recognize this and not duplicate them.
But potential duplicate issues can arise if there are edits or metadata changes on the Mac. Or, the Mac Photos app contains photos imported from other sources (like an SD card) that also happen to be on the iPhone.
So here is what I would try (NOTE the backup of the photo library just in case!!!)
On the Mac, open Photos > Settings > General tab and confirm which library is set as the System Photo Library. You want the System Photo Library to be the Library she sync'd her phone photos to. Also, ensure Optimize Mac Storage is not enabled (so you’re working with full-res originals locally).
Next back up this library just in case - maybe twice (TM and somewhere else!) Then, on the Mac, enable iCloud Photos first under Photos > Settings > iCloud.
Wait for the Mac library to finish uploading to iCloud (it can take hours or days). Check that the Mac upload to iCloud is done by looking at the status at the bottom of your library in the Photos app, it should say "Synced with iCloud Now (or some other time)" I would also check on iCloud.com and make sure the photos and videos numbers are very "close". I just checked mine, I have ~51,000 photos, and the iCloud is 2 off. Oh well.
Only after you have backups, and iCloud is correct, then enable iCloud Photos on the iPhone. As I said before there *could* be some duplicates for the reasons I outlined. The Mac photos app and third party apps can be good and finding duplicates after it's all set up.
That should be pretty safe?!?!?!