Assuming they're wanting to excise the slavery aspect, I might be inclined to make Neogi ruthless gourmands who love to feast on humanoid flesh - that way they still have motivation to hunt people down, they'll still be almost universally hated, but they probably won't be quite as much of a hot button issue.
I'm actually a little disappointed at the answer re:Illithids. One of the more interesting aspects of the original Spelljammer was the ambiguity surrounding that race - it wasn't quite as obvious as before that they were monolithically evil. They're very much the Vorlons of the setting.