It will probably be a problem, since any edits, like even changing the name, result in a new file. You could remove the photos from the libraries and then Finder copy over one or more the folders, since Finder would ask about overwriting dups. But if you've got a lot of photos this will be a pain.
Take a look at iPhoto Library Manager; it can merge libraries. It won't necessarily automatically remove duplicates, but it can make it easier to do it manually. And it allows you to at least manually sync and manage the libraries.
I use Aperture more than iPhoto, and it has an import feature that allows you to avoid importing duplicates. Not sure if iPhoto has that, but check. And it might be a reason to get Aperture.
Rob