Quoting Wikipedia: "Honey is a sweet food made by bees using nectar from flowers." "In the hive the bees use their "honey stomachs" to ingest and regurgitate the nectar a number of times until it is partially digested." "...the nectar is still high in both water content and natural yeasts, which, unchecked, would cause the sugars in the nectar to ferment." "...bees inside the hive fan their wings, creating a strong draft across the honeycomb, which enhances evaporation of much of the water from the nectar. This reduction in water content raises the sugar concentration and prevents fermentation."

Partial digestion, plus enhanced evaporation. That's not "slightly."

If you want, you can argue that there's a continuum. Orange juice comes directly from oranges, but most olive fruit cannot be eaten without processing to remove bitterness. Milk comes from cows (okay, and other mammals) and cheese comes from milk, but it's hard to say that cheese comes from a cow, since other factors are involved. Does beer come from barley? No. Beer comes from the beer maker, who uses various ingredients, including yeast.

So yes, honey comes from nectar, but the essential transformation which makes it be "honey" is done by bees. Therefore, honey comes from bees just like beer comes from the beer maker, and cheese from the cheese maker.