It wasn't Taylor it was Piller who wrote this episode.
Jeri Taylor wrote Chakotay's back story.
And I think you are being overly sensitive and reading far, far, far more into the idea of the backstory of Indians being part alien. Sometimes a cigar is just a cigar.
And, yanno, just like some Irish took offense to "Up the Long Ladder," so I do to Akoochimoya and all that crap.
If you're going to show an ethnic group in the future, it helps not to make it a bunch of tired stereotypes.
That's all Chakotay's ethnicity is--a bunch of old stereotypes. Tribe Hollywood.
YMMV and obviously does. To each his own.