The issue with the Quincy was that they refused to stop destroying Hollows in massive numbers and let the Shinigami cleanse them, thereby jeopardising the balance between Soul Society and the Human World. Kido users are Shinigami and can chose between using Kido or using their Zanpakuto. They can chose to finish a Hollow off with their Zanpakuto and they are not destroying Hollows in massive numbers - thus they are not jeopardising the balance.