The reason for the ludicrous decision can be summed up in two words
Danny Alexander
That argument would hold more weight if Leuchars wasn't in the constituency of Sir Menzies Campbell, a former Lib Dem leader and a man of great personal influence - I can't see that Danny Alexander would have done his long-term prospects* much good by making a direct intervention in the face of an elder statesman of his party...
I think a more likely reason is that the economy of Moray is highly dependent on its military units. Basing aircraft there demonstrates long-term commitment; army units are much easier to move and would have left question marks over the area, particularly if the Army started having difficulties finding training areas. Meanwhile, Fife can quite easily survive without a military presence.
* - his personal long-term prospects within the party. The long-term prospects of Lib Dems in government are not high on anyone's agenda!