Crooksin
Glue Sniffer
The only reason Ulfric is called out more on his racism that, say, Rolff, is because he is a jarl. If the people of Skyrim hate the Khajit, then I say the racism is more just because of the setting. Does not make it more right, just shows that the time it is set in is different that today, and that people blindly use today's morals instead of saying "this is medieval times, stuff like this is going to happen." and finding more logical reason to join one side or the other.
Racism may be more accepted in Skyrim's setting, buts its still not completely accepted. The Empire certainly does not enforce racist policies like Ulfric or the Stormcloaks do and the Dark Elves definitely don't enjoy it, either.
That's besides the point anyway, please explain your last analogy comparing Necromancy to racial segregation of the Dark Elves. How would segregation be better in the long run for anybody, except the Nords of Windhelm's egos? Necromancy is a tool and therefore can be used for many things, good or bad, while segregation is a policy but I am curious to know how it could be for the benefit of the Dark Elves or Windhelm like you suggested.