You’re right that the attempt wasn’t necessarily malicious. I feel it can be possible to have good intentions and still end up doing something wrong, whether that be sexist, racist, or otherwise hurtful.
Inaccurate cultural depictions can take away control of a people’s story and misrepresent them in such a way that distracts from the fact that they are a present-day people living their own everyday lives.
Of course, I think the failures in Chakotay’s character development that you mention are also very real and are a major factor in the failure of his character.
Overall, though, I still quite enjoy Voyager.

Also, I’m pretty sure this episode contains the first live action appearance of an Edosian, first introduced in TAS and appearing in ever animated Trek series since.