I get your point -- but neither Yamataians nor Nekovalkyrja are technically human in the traditional sense -- more like biological androids. Yamataians would still be closer to Neko in my view than traditional human's like Nepleslians or even Geshrin due to their inherently artificial nature and very different capabilities.
I mean, they mass produce most of their members (even some Yamataian player characters are 'manufactured'), switch bodies as the need demands or when better bodies become available and can virtually resurrect themselves from death at need. I think most Yamataian's/Neko would view their bodies as little more than tools at this point, considering the nature of their culture.
Though I also imagine there might also be some neko who hold a dim view of those who weren't born true neko, and some Yamataians that view changing bodies unnecessarily a negative thing -- they are 'descended' from humans after all. There will always be those who are biased against those whom are different from themselves, who dislike unneeded change, or view themselves as innately superior for whatever perceived reasons, or are just plain envious.
If the empire was still dominated by the virtually human Geshrin, it might be easier for me believe Emiko would take such a view. Normal humans would probably look at it in the way you suggest -- if she had been raised solely in one body from birth, I could understand more reluctance to change into a neko body. However, having been raised as part of a culture which has already performed one universal 'upgrade' and has for decades had members used to the idea of switching bodies like a suit of clothing, I doubt most would have significant qualms about the idea. She'd already would have changed bodies once, going from Geshrin to Yamataian with most of the other Star Empire population -- having done it once and experienced first-hand what such a change is like, what's one more time? If she disliked the differences -- which would be doubtful as who would really mind having overall increased abilities -- she could always change back if she so desired.
--Besides, having a formerly more human character change bodies from a civilian body-type to one designed specifically for war, was one of the most interesting things I thought to explore in RP for the characters development.