While I am not fimilar with that adventure, once I would of put a stop to that behaviour once the player starting going around attempting to execute command staff. Any character can be abused in my opinion, and it it up to the GM to discourage the player from this type of behaviour, subtly first, and more aggresivly if the player doesn't take the hint.
While Commissars are within their right to perform summary executions within the rank and file of the Imperial Guard, I would not say they can just blindly go around executing command staff. They are are a lot harder to replace, and removing an entire command crew would seriously jepordize Imperial interests, as you are well aware with the effect it had on your adventure.
Commissars are front line soldiers, and if they feel a field officer to be should be found wanting, they can temporarily take over command and summarily execute any soldier they feel is jepordizing moral. But one is not necesssarily for the other. If a Comminssar were to abuse his powers and piss off an entire platoon or company for that matter he would be putting a huge target on his back. Most IG distrust Commissars by nature, and having an entire company hate you and want to see you dead is not in the Commissar's best interest. He still has to eat, sleep and fight with these man. As others have pointed out, all sorts of 'accidents' could occur. or outright assinations.
In terns of Command Staff, Commissar' s only out rank anything below Reginmental Commander, anything higher( Lord Marshal, Captiain General, Lord Castellan) are going to take serious issue with a political line officer removing their support staff without a damn good reason. If things get out of hand they can even peition the Commissariat or a Lord General to intervene. A PC Commissar is by no means on par with a Lord General, and the Commissariat is not going to let one of their own ruin their privlidged position by running roughshod.
Point being, the Imperium of Man is huge empire that centered on bureaucracy. With so many branches and organizations, very few individuals have the kind of authority to just do as they please, and a Commissar's duty is to the troopers, if he goes around killing the upper echelon of the command structure, who is going to take their place? Not the commissar, he's duty is on the front lines.
"They have authority over both the soldiers and regimental officers. Commissars have both the right and duty to immediately execute any Imperial guardsman or officer who shows cowardice or incompetence in battle." (http://wh40k.lexican.../wiki/Commissar)
If a commissar can give a valid reason that someone must be executed, even a high ranking individual, they should be allowed to. Yes every class can be abused however commissars are much easier to abuse based soley on story rather then abuse based on rules.