Chakotay wouldn't have been able to "hold the crew together" if Janeway hadn't integrated him into her crew in the first place. The Maquis were considered terrorists and enemies of the Federation. After all, her mission had been to apprehend him and his crew. Janeway could have easily decided to keep the Maquis in the brig. Instead, she had the foresight to offer Chakotay the position of second in command (which should have gone to Tuvok if she had followed protocol to the letter) and to assign his crew to key positions on the ship. B'Elanna would have never been Chief Engineer without Janeway's approval.
She also integrated into her crew aliens and a former Borg drone. Let's not forget that it took Chakotay a long time to accept Seven as one of their own.
I think that they were an excellent command team and played well off each other. Kathryn was more impulsive, but understood science and engineering in a way that Chakotay didn't. Chakotay was more sedate and was a good foil for Janeway. Voyager was in a unique position, they only had each other for support. If they hadn't trusted each other's instincts they would have never made it home. Even during their worst arguments there was no doubt that there was respect and affection between them. Either one of them would have been devastated if something terrible had happened to the other. I'm not sure that Voyager would have survived the seven years in the Delta Quadrant with a different command team.