First of all, Chakotay never stated that he was a vegan. In "Unity" he said "I'm a vegetarian".
Not to mention that the comment itself may have been some sort of joke, regarding the fact that Riley said something about longing for Texas steaks and regretted that she couldn't offer Chakotay something similar.
The pathetic thing is, I don't know of any Native American tradition that includes vegetarianism. Eating meat is part of the cycle of life. Turning NAs into vegetarians is Jeri Taylor slapping her New Agey nonsense on us.
I agree on that one. Sometimes Taylor's own views did creep too much into the stories. There are some examples of that in otherwise good books like "Mosaic" and "Pathways" too.