Use pyicloud to delete all photos from iCloud (may need to be run multiple times)

delall-icloud-photos.py

#!/usr/bin/env python
from __future__ import print_function
import json
import sys

from authentication import authenticate
from future.moves.urllib.parse import urlencode

if __name__ == '__main__':
    username = sys.argv[1]
    password = sys.argv[2]
    smtp_username = smtp_password = smtp_host = smtp_port = smtp_no_tls = notification_email = None
    print('Logging in')
    icloud = authenticate(username, password, smtp_username, smtp_password, smtp_host, smtp_port, smtp_no_tls, notification_email)
    photos = icloud.photos.all
    operations = []
    url = '{}/records/modify?{}'.format(icloud.photos._service_endpoint, urlencode(icloud.photos.params))
    headers = {'Content-type': 'text/plain'}
    seen_record_names = []

    for photo in photos:
        # Avoid duplicate operations
        if photo._asset_record['recordName'] in seen_record_names:
            continue
        seen_record_names.append(photo._asset_record['recordName'])

        mr = {'fields': {'isDeleted': {'value': 1}}}
        mr['recordChangeTag'] = photo._asset_record['recordChangeTag']
        mr['recordName'] = photo._asset_record['recordName']

        mr['recordType'] = 'CPLAsset'
        op = dict(
            operationType='update',
            record=mr,
        )
        operations.append(op)

        # Limit to 100 photos at a time
        if len(operations) >= 100:
            post_data = json.dumps(dict(
                atomic=True,
                desiredKeys=['isDeleted'],
                operations=operations,
                zoneID={'zoneName': 'PrimarySync'},
            ))
            print('Deleting 100 photos')
            print(icloud.photos.session.post(url,
                                             data=post_data,
                                             headers=headers).json())
            operations = []

I just had a similar issue. Made a quick script to do it :
https://github.com/zakirangwala/icloud-photo-manager