The humans were not the aggressors in the 1000 year war. The fairies didn't have the capacity to fight back against the humans, and to the humans, harvesting Fae Life Energies was just like harvesting any other natural resource to ensure continued human dominance. The actual 1000 year war only began when the Guardians attacked the Humans to punish them and protect the fairies and the war didn't end until the last fairy was freed from magical captivity.

Having been forbidden from entering the forests and without any magic to fall back on Human civilisation evolved rapidly to what you would consider more or less modern standards.

The Humans legitimately didn't think they were doing anything wrong.