Apple - how to delete already imported pictures from iPhone in MacOS X Photos app?

Have you tried using Image Capture?

Plug in your phone. Select it from Devices. Select the photos, hit the little "no" icon (the circle with the line through it) near the bottom of the window, and delete the photo. Also good to delete photos you don't even want in photos.

If the identical images are already present in Photos (due to prior import from My Photo Stream, for example), it will not reimport them. It only imports new items. In fact, the button on the import screen in Photos says "Import All New Photos" if there are already-imported photos present on the device as well.

There is no way in Photos to remove already-imported photos from iPhone, like there was in iPhoto. The only way is to remove them by using the Photos app on the device itself.

Try disabling iCloud Photo Library on your phone. I had this enabled and was wondering why the "Delete items after import" icon was missing and Image Capture showed a lock icon against all of the items and hid the delete button.

Once I disabled iCloud Photo Library, disconnected my phone, reconnected and restarted Photos and Image Capture, the delete icon reappeared.

A workflow I do is to go back and make sure I reselect all of the photos, check "delete items after import" and re-import them again. I'll have duplicates in my album, but I feel safer that way.

Further reading: http://www.howtogeek.com/219092/why-cant-i-delete-photos-off-my-iphone-anymore/