With Thaumcraft 3.0.5a, Natura 2.1 beta 1:

Straw golems harvest fully grown cotton correctly, however, they will also be harvested when the flowers are still pink. Fully grown barley is completely ignored.

When a smart golem harvests cotton when the flowers are pink will replant it with barley.

This has been addressed on both ends. Hopefully golems will be sensible now.