To answer the question of the title, ultimately -- yes.
Zodiark was functionally a tool, and like most tools, it is not inherently good or evil; but ultimately wound up being used for evil purposes, despite being created to do something that initially had good intentions. I think Hades makes it pretty clear at the end of Endwalker by saying their methods wouldn't have ultimately worked; so despite being created to stop an apocalypse which was Objectively Good, once you get further into the subsequent sacrifices where it goes from being willing Ancients offering themselves to forcing your ritual sacrifices onto life you deem "unworthy" or "less than", esp. post sundering, it's pretty clearly Not Good and Very Evil. While the Capital "E" Entity of Zodiark may not have possessed the will for most of it's creation to order people to do explicitly evil things (especially post-Elidibus removing himself), I think it's pretty obvious both explicitly and on the margins that its influence was directly responsible for a lot of Bad Things.
