If it's a job requirement to book via the agency, then there isn't a way around it. I'm in the same boat.

My co. used to be loose about the requirement by saying if we could find a cheaper fare than what the agency could get, we could book it. Therefore, I was able to direct-book at AA.com with a 10% off code and always beat the agency by a few bucks. I was pretty diligent, printing out the fare comparisons to prove that I truly was saving money.

Then my co. changed its stance and now all travel must go through the agency. Easier on them administratively, I'm sure.