The standard counter to pachiderms is MR targeting spells, soul slay & enslave mind are particularly devastating.

Targeting their morale can also work: missile troops backed by fear causing critters or spells (terror, panic...)

Other options: high defense troops boosted with body ethereal will be highly resistant to being trampled. A size 6 SC cannot be trampled at all, and the elephants have to fall back to their subpar combat skills.