The Mk VI was being tested, they probably didn't intend for it to go live as soon as it did, but when reach fell and the covenant were on their way to earth, you can imagine the unsc would want every single little advantage they can get, even if that means outfitting only 5 spartans with it. Lord Hood was always a big believer of the spartans so he may have personally requested it.
[Edited on 02.22.2011 2:15 PM PST]