Never use iCloud as a storage device for photos.
You should be importing all pics taken with the iphone to your computer regularly as you would with any digital camera. This is covered in the manual.
Once you have stored the photos on a computer, then you can delete them from the phone.
A backup should not be thought of as a storage device where you can save and extract photos to and from a device. The only good a backup is, is when your device get corrupted/dies and you perform a restore to get most everything back to the replacement or fixed device. To restore a backup, your device must be wiped completely before doing a restore of everything. You can't selectively restore specific files.