Well, to be fair, Chakotay's spirituality was handled poorly most of the time. Do you recall he was a vegan? No? Neither did the writers three episodes later when he's hankerin' for a steak.
They never established him as a vegan--just that he didn't eat meat.
That went back and forth...
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.
So, yeah, I agree. Chakotay's spirituality was handled poorly 99.9 percent of the time.