Just want to share another option:
# mark two objects to be deleted
session.delete(obj1)
session.delete(obj2)
# commit (or flush)
session.commit()
http://docs.sqlalchemy.org/en/latest/orm/session_basics.html#deleting
In this example, the following codes shall works fine:
obj = User.query.filter_by(id=123).one()
session.delete(obj)
session.commit()