While the magi of Diedne certainly had their versatility thanks to their natural talent with Spontaneous Magic, in terms of usage in total war, Formulaic and Ritual Spells would be king since the higher-level defensive and building spells and better Penetration in attack spells would be paramount. House Diedne would certainly have stability advantages and probably have somewhat quicker reactions, as they don't need to take the time inventing or learning most of their lower-level effects for repairing infrastructure and stuff, but that advantage is somewhat limited, not even accounting for its comparison to the rest of the Order's potential advantages.
So the main battle comes down to a group of magi with no special unifying advantage(s) Formulaically or Ritually going against another group something like 10 times its size, with several unified forces bringing specific group advantages to the table. And of course, the remaining Order also had way more resources and presumably controlled a lot more land. More magi also equals more exotic specialists (infiltration to retrieve Arcane Connections, anyone?) and more, probably stronger groups for performing powerful rituals to basically break the Diedne and prevent their own breakage.
I just can't imagine how the Order didn't utterly steamroll the renounced Diedne magi with only moderate trouble. It doesn't seem like it would be the long, horrifyingly bloody war it's made out to be. Can someone fill me in on the part I'm missing?