Hero engineers.

Perhaps the most effective way for a Machine Guild to counter a rush is with an ice block combined with deadly cold, provided you have the ice block available in the guild and have chaos magic. In the late game, you can also spend a turn or use troops that attack multiple squares to engage, or use an area-of-effect spell, etc. Mages can learn the "Control Machines" spell, although this will leave you without your rapid-fire ballista, but the chance to take control of the enemy's ballista, which they are relying on, is encouraging...