You'll need to be a lot clearer about where these photos are. Generally speaking, deleting photos from photostream deletes them from all devices.
Photos you've taken with the iOS device are also available on Camera Roll, so deleting them from Photostream doesn't really matter except to change the way said photos or videos get to other devices.
On my setup, I generally import pictures I've taken with my camera to my MacBook Pro. I have photostream set up so that ONLY images I *drag* into the photostream folder are shared with my other devices, not added automatically.
On my iDevices, all pictures TAKEN on those devices are added to Photostream automatically. This setup has the practical effect of only manually selected pictures being sent "downriver" from Mac to iOS, but all iOS pictures are automatically sent "upstream" to the Mac.