I took a look at this. When the ombudsman's office was created, it was created so that there was a separate entity from the chain of command that members of the Canadian Armed Forces could go to to have their concerns heard and action could be taken independent of the chain of command.
Also, the ombudsman's office does a lot of other work as well, for example, taking a look at members' issues of pay or other types of issues that need to be changed to give the minister the advice. The role of the ombudsman is actually to give advice to the minister, not the other way around.