If you want to fly the non-city pair airline on a particular route, you'll have to provide a good justification why to your agency's travel office. Frequent flyer miles/maintaining elite status is not a valid justification.

Usually, the city pairs are the cheapest fares offered on a route and are usually refundable/fully changeable tickets, in contrast to the non-city pair flights. So, if you're generally flying routes that Delta won the city pair contract for, you would be fine. However, if you're flying routes that Delta did not win the city pair contract for, you'll need to provide good justification on why to fly with that airline/that particular flight if the city pair flight is still available.

Link: http://www.gsa.gov/portal/category/27228