chore(librarian): update configure_state_yaml.py to avoid duplicate entries

[parthea]

This PR resolves the issue where duplicate values for id could be added to state.yaml. When duplicate entries exist in state.yaml librarian seems to provide an empty generate-request.json which leads to the following error (see googleapis/librarian#2186):

Traceback (most recent call last):
  File "/app/./cli.py", line 261, in handle_generate
    request_data = _read_json_file(f"{librarian}/{GENERATE_REQUEST_FILE}")
  File "/app/./cli.py", line 100, in _read_json_file
    return json.load(f)
  File "/usr/local/lib/python3.9/json/__init__.py", line 293, in load
    return loads(fp.read(),
  File "/usr/local/lib/python3.9/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/usr/local/lib/python3.9/json/decoder.py", line 340, in decode
    raise JSONDecodeError("Extra data", s, end)
json.decoder.JSONDecodeError: Extra data: line 31 column 2 (char 755)

See output below for google-cloud-dlp and google-cloud-eventarc which already exist in .librarian/state.yaml

partheniou@partheniou-vm-3:~/git/google-cloud-python/scripts/configure_state_yaml$ python3 configure_state_yaml.py 
Skipping package 'google-cloud-dlp' as it already exists in state.yaml.
Skipping package 'google-cloud-eventarc' as it already exists in state.yaml.

[jskeet]

Yup, this is what we do in the Go stategen tool.