I think you might be referring to virus replication outside the body, not inside the body. If that's not the case, do you have a source for that?
There is usually no damage from a high fever, unless it's prolonged. Kids also do better with fevers, and the standards for when a fever might become dangerous is different for children than for adults.
Studies have been split on whether treating a fever prolongs an illness or not, so it's up to you, really. If your child had a temp of up to 41, they had to have been feeling terrible, and at that point, I'd have done something to just relieve their discomfort. Your choice may be different.