Still its relevant when it casts it in relation to counter strike.
Is it possible to give it -2 dice before it hits back?
The ability takes effect during the "Damage and Effects" step. During this step it immediately cast the spell, and by the rules of placing an enchantment, you can reveal immediately.
So anything that happens after that step is subject to the curse laid on them.
Where it gets a little weird is that the ability requires the target to be damaged from the attack, and remember that enchantments cannot effect an event that has already happened. So for example,
Sectarus rolls 2 damage and you have the option to cast the curse, "Rust" and reveal it immediately. Since we are still in the damage and effects step the target does lose 2 armor, but since the damage has already been done, as per a condition to cast the spell, the attack does not do two more points of damage.
To specifically answer the question, yes you can put an agony on a target and that curse effects their counterattack.
Curiously however you can also, under the effect of a battle fury, place a marked for death on the first swing and not get the bonus on the second attack; that is a marked for death wording thing though.