The Forerunners being able to fight off the Replicators makes more sense if you look into the Reclaimer saga arsenal, most of which uses either Hard Light (and thus behaves a lot more like bullets than Energy Weapons) or particles that vaporize the target, leaving nothing for the replicators to absorb. And more to the point, the Forerunners fought the Flood, who are an organic version of the Replicaotrs - they knew what to prepare for.
