python3 -c "import pathlib; [p.unlink() for p in pathlib.Path('.').rglob('*.py[co]')]"

python3 -c "import pathlib; [p.rmdir() for p in pathlib.Path('.').rglob('__pycache__')]"

Или при помощи find:

find . -type d -name __pycache__ -exec rm -r {} \+