You still have a brain, don't you? You can think for yourself sometimes, y'know. [ He scoffs. ] Just because somebody's a higher rank than you are doesn't mean they know shit. Take my former boss, for example-- there's a reason why I got his job.
[ That reason was murder, but shhh. Shhhhhhh. ]
People call it arrogance when they know you're right and they're wrong, buddy. It's a way to try and shut you up by making you out to be the bad guy.

[ Okay, so-- this guy was clueless on a few more things than expected. He could work with that. It was just a little explanation, after all! What was the worst that could happen? ]
Means that because you have a conscience, you object to...something. Usually military stuff, but I've seen it used elsewhere before-- although that would fit you without much modification, wouldn't it.