If there aren't many photos, the easiest way to do it is simply delete the photos on the phone. Unfortunately, this means selecting each photo individually as there is no 'select all' option.

To avoid individually selecting photos on the iPhone, you'll want to use the 'delete' option when prompted at the end of importing. Because iPhoto only deletes the photos that were imported at that time, you won't be able to do this with your 'normal' iPhoto library. To get around this, simply create another (throw away) iPhoto library to import the photos. Select 'delete' when prompted at the end of the import to delete the photos from the iPhone. Then you can delete this throw away library on your Mac.

To create a new iPhoto library, hold down the Option ⌥ key when launching iPhoto. This will display a window asking which library you would like to open or create a new library.

You could use OmniDiskSweeper (free to download and use) to search for and remove big folders. To find the problematic area fast, run it in parallel on both your macs (to see the differences) and start at the top level.

If you don't want to install additional software, you can start by running du -sg /* on both Macs, drilling down into the directories with the biggest difference and repeating du until you found the problematic files.