I don't have an iPhone, but on my Lumia 1520, I set my photos to automagically backup to OneDrive (when on WiFi). Then occasionally, I go into Photos and delete photos on my phone.
I can choose if the Photos app shows photos from the phone, OneDrive or both, and, when I delete, it offers me the choice to delete the photo on the phone only or both the phone and on OneDrive. If you delete on the phone only, it won't "sync back" from OneDrive to the phone.
Very slick, actually. Hope that helps.