Also, it's Chandler's ship. I feel like he needs to control everything that happens on it. He makes the decisions, he continues to adhere to the strict Navy code (even thought it may not exist anymore), he unnecessarily goes out on missions when he could leave it to the people who are actually supposed to do it. Heck, even the President defers to him. I'm not surprised that he's irritated when Rachel does what she wants to do without consulting him.
I think one of the issues with this whole story-line is the method of execution. If the Niels had been stabbed to death, then fine do an inquiry. It would have opened up (albeit in a Murder She Wrote kind of way) the list of suspects and put the perpetrator in doubt. But with Niels just dying and all 3 doctors agreeing, there was no real reason to continue with an investigation.
I also think that they were trying to play up the perception of control on Chandler's part with the reality of how his sailors live their lives. Potential sex in the bathroom, Foster & Green, rumors of the "hit" on Niels all were trying to show how he really can't control every aspect of their lives.