using pestilence

The most obvious use is to throw the spell into as big a pack of the enemy as possible, so it will spread.

However, you can carry it much further, by giving it to one of you own creatures, and then sending that creature into the enemy camp to pass it on!
Better still, if that creature is undead it will not be harmed by carrying the pestilence.

defeating pestilence

Some creatures are immune to pestilence. Since pestilence will be carried by creatures with flesh, wooden dryads, and the resurrected spirits of the knights will not catch it.
In addition, undead creatures will not be harmed by it.

Heal, used directly or via the totem of life will remove pestilence from an infected creature.

And like any other enchantment spell, pestilence can be instantly removed with disenchant.