Somepony, at some point, is going to win this campaign. Only way to do that (in true 40K fashion) is to beat everypony that opposes them. Would they just have to destroy the entire fleet? How exactly would this force be driven off of the planet?
Realy, any long-range weapon in large numbers could snipe off most of this army. As I posted, this army is low in numbers but is filled withvery powerful individuals. The whole thing relies on the existance of a few key groups of units. If one is lost, they lose any advantage they could have gained from it. They dont have any land transport, and by fleet I mean 2-3 ships, max. Alot of the heavy hitters are not as duriable as one would expect, so a machup against the Duo would be nearly impossiable to get out of without heavy losses.
They dont have to be limited to enquines. Acid spitting insectoid giraffes and armored tankish elephants could all be nasty things.Carnifexes, Trygons and Other Big Things: Pretty much the same as warhammer canon, or some other large scary monsters.
Everything in between: Ponies, but often with added spikes.