Tracking this back to the root makes me think disabling iPhoto's automatic download/import will solve the issue.
You can still keep the Photostream enabled, but you would have control to highlight the photos in it that you actually want to import and click 'Import Photo.' Or, highlight all the photos you don't ever want in Photostream, delete them from the Photostream, then afterwards highlight everything an select 'Import.'
Yes it's a bit more manual, but there aren't a lot of shades of gray with iCloud.
I won't go as far as to suggest turning off Photostream though - it's an adequate last-resort backup, and when you delete photos from your iPhone camera roll, those photos won't actually come back to your iPhone, so there's no worry there.