I run into this all the time. Negotiated rate on preferred airline is sky high, low fare alternative presented by TA is comparable to online bookin at preferred airline.

My solution, go to my boss and lay out the facts, tell him if I book on my own I save so and so dollars and get to the site that much quicker.

It usually works.

that said if the price difference is more than $75 I usually go with the cheaper of the 2.