I'm not talking about the "we work for the inquisition" issue, my players are fully aware that waving that flag around can cause more problems than they want. I'm talkinag about one person being an Arbites, judge, jury and executioner and all that...I feel that almost every intimidation check he makes versus an Emperor fearing civilian would end up getting plus modifiers.
Another is a Techpriest and even if he is a minor part of the Cult Mechanicus he wears the red robes and not many outside of the cult would know how high or low he would be. Also using the standard requisition rules he managed to start out with three mechadendrites due to those things being scarse for members of the Adeptus Mechanicus...but that's a whole different issue.
Then there's the player who plays a member of the Adeptus Ministorum. Even the nobels (unless corrupt) are religous, Emperor fearing and superstitious and would hold a priest in some regard. Lucky for me the player is not all that familiar with the setting and is unaware of the sway his character could hold over the masses. He just knows he's a good talker who can hack someone apart with a chainsword.
How do you guys deal with players being in somewhat of a powerfull position?