While some agencies do say you cannot use miles to upgrade official business travel, you are clearly within your legal rights to do so. All civilian travel is governed by Joint Travel Regulations, JTR, Volume II. The State Department is the responsible agency for establishing civilian travel policies. The JTR specifically states that FF miles may be used for upgrades and "amenities available to the general traveling public...that contribute to the benefit of the government." Surely, anything that makes your travel easier makes you more productive upon arrival at your temporary duty station and benefits Uncle Sam. If your travel folks balk, either work the upgrade yourself after ticketing is done or have the question run up the legal flagpole. Good luck.