Q: keep photos on icloud but delete them from iOS device?

You can't store photos in iCloud and delete them from your device. Deleting them on the phone also removes them from iCloud. You can set to optimized storage on your device which compresses the resolution  of device stored photos, keeping the originals in iCloud. 

If you want to be able todelete photos from your phone and store them elsewhere, you need to use subscription cloud storage such as Dropbox or store them on your computer.

iOS: Importing personal photos and videos from iOS devices to your computer

What about turning off the iCloud for the phone then manually  transferring photos to the computer - if you turn on the cloud again will it delete those photos (wanting to sync things such as notes - or can I turn off cloud just for photos on my iphone5s 9.3.1

You can just turn off iCloud Photos in Settings/iCloud. It won't delete the photos. They will be downloaded again.