I think this assumption is false:
Presumably the One had encountered and destroyed an Agent like Smith in previous versions of the Matrix.
Agents are incredibly difficult to destroy1 because they can simply leave the body they are possessing if they are "killed". Moreover, destroying an Agent is usually overkill -- as long as the Agent runs out of nearby bodies to possess or the Zion operative can escape the Matrix, there's no need to attempt to destroy the Agent. Notice that Neo didn't bother trying to destroy any of the other Agents he encountered later -- he simply "killed" them or escaped from them.
The only Zion operatives who stand a chance to destroy an Agent are the Ones, and there aren't many of them. It's quite likely that none of the Ones before Neo destroyed an Agent before.
It's also worth noting that Neo is particularly special, even among The Ones. The Architect notes that previous Ones were designed to be profoundly attached to the human species but Neo is profoundly attached to a particular human (Trinity) by love. Consequently, Neo is the first One to choose not to return to the Source. Neo broke the cycle that the previous Ones had allowed to continue, and became more powerful than any previous One. The Oracle explains that, as a result, Smith has become exceptionally powerful to match Neo's power:
[Smith] is you. Your opposite, your negative, the result of the equation trying to balance itself out.
In short, no previous One had ever destroyed an Agent before, and previous Ones always chose to return to the Source whereas Neo chose to return to the Matrix. This led to the unprecedented situation in which Smith became a virus powerful enough to potentially destroy the Matrix.
1By "destroy" I mean that the Agent is forced to choose deletion or exile. Normally Agents are merely "killed", in which they are merely forced to possess a different body.