I'm not against you Becca, but I have two points as devil's advocate, or at least, why bother making a scene about it now?
First, your name and appearance don't match. You might be able to lodge a complaint, but why, because you were called sir several times (maybe dozens) over the course of a conversation? The ladies that helped you were following convention, you're registered as male, under a male name, they were calling you by your legal identity. They were not doing anything illegal, even if it was wrong.
Second, your perception of how things went makes it sounds like what they were doing was genuinely hurtful, which I am sure it was. I've been there, done that, and I know what it's like to cry for hours afterward. It sucks, and my heart breaks for you. However, your perception alone isn't going to be enough to get any traction out of the dean's office. You can't say that "they made you feel bad" if you try to complain. I don't think I'd even bother. You need to have said something, corrected them or whatever, and then you can say, "I asked nicely and they refused to treat me with respect."
Best advice I can think of: go back and get your business taken care of. If you get hassled like you did the first time, if they call you sir, then out yourself to them. You're already outed anyway: you dress like a girl, but have a guy's name. Tell them that you're trans, and you'd appreciate being addressed properly.
If the person helping you refuses to address you as you've requested, you actually CAN go up the chain of command until you find someone who's not an a$$hat and will actually help you AND be nice to you. You'll also have more standing to make a complaint-- you asked, corrected gently on what you prefer to be called, and legal status notwithstanding, if you're refused, well that's a problem you can take higher up.
I'm so sorry this happened to you. I hope it gets better, and my advice: be bold, and don't be ashamed about who you are. Always be careful, but never be ashamed.