I think you need to think in two parts of the punishment. First the preventive messure, and then the corrective one.
This punishment think can be the seed of a nice story. For example, when i had a similar situation, my inquisitor decided that all the retinue, except for the most responsible member, will wear an explosive collar from now on. Now that all the PC are mad against the "bad desition-taker", the inquisitor says: "Now is the time for you to decide your brother“s faith. As the Left Fist of the Emperor is your right and your duty to do so. I want him alive, because I still have plans for him, but be fair or my warth will be against you"
This idea will give allow you to have a very interessting trial. I have 7 PCs in my story and belive me that 6 heads thinking about a punishment are better than one.
Always remember that the purpose of everything in the RPGs is just to tell a cool story and have fun.
Keep rolling!!!