There is a lot of incorrect web advice on iPhone image deletion. Some of it is dated, some of is recent regurgitation of old methods that no longer work. None of the articles I found differentiate between the behavior with iCloud Photos enabled or disabled.
If you have iCloud Photos enabled there is no efficient delete method from the iPhone. That’s because Apple doesn’t want us to think about photos being on a device. Devices are only temporary stores; the true home of a Photos is in iCloud.
You can't use Aperture to delete after import. You also can’t use Image Capture (at least not from El Capitan). Aperture will offer the delete dialog but they will remain. In El Cap Image Capture does not show the delete option. I don’t believe Photos.app on Mac or iCloud will allow one to delete images that are ‘temporarily’ stored on a specific device — that really doesn’t fit Apple’s photo model. Again, the true home of a Photo is iCloud - device residence is a form of transient cache.
From the iPhone you can view the all photos album, scroll to bottom, select an image then slide up until all are selected, then delete. Apple doesn’t offer a delete all option because it knows iCloud Photos is confusing and, given half a chance, people will delete their entire photo library. Note this is only a first stage delete, you do this you have to go to recently deleted and empty that as well (“trash” equivalent).
With iCloud Photos disabled delete works from both Aperture and Image Capture.
I have experimented with using photo stream sharing from Aperture and iCloud Photos from Photos.app. It’s awkward and I periodically need to reenable photo streams in Aperture, but it has worked. I’ve decided it’s not worth the delete complexity though. For now I’ve turned off iCloud Photos and I’m back to old school wired transfer form phone to Aperture. I continue do iCloud photo stream sharing from Aperture and I subscribe to those on my iPhone and Aperture.
PS. With iOS 10.1.1 I saw some quite odd behavior after I disabled iCloud Photos on the iPhone. Even though Photos.app showed no images Image Capture showed many. I had to do a forced restart of the iPhone (deletes some caches) to clear out those ghost images.