How could it kill the MJOLNIR armor, when it wasn't an extension of the MJOLNIR program? The Spartan II's were developed for the One-man-army, nothing-is-impossible type soldier. The Spartan III's were top secret, Section 3 infiltration units. They were never meant to be better or worse than the Spartan II's, but were Colonel James Ackerson's way of "Winning the war", and getting back at his rival Dr. Catherine Halsey. So they don't really kill the MJOLNIR armor, but more attempt a different strategy.