Holmes did say to Bell in the final scene that the Commissioner had decided not to take the recommendation, so he and Watson are still permitted to work with the police. Based on that, we can deduce
that Bell advised the Commissioner not to suspend H&W. However, he's evidently still bitter toward Holmes on a personal level, so I'd assume his recommendation was based on professional considerations, the good that H&W do on the whole. Whether he'd be comfortable working directly with them in the future is another matter.