You can't really blame the current Germans or Poles for existing more or less and yet CEV still doesn't attempt to adjust for this, which seems to violate normal moral intuitions about consistency.

I don't see any violation of moral intuitions there. It isn't the business of CEV to second guess what morality should be. It works out the morality (and other preferences) the input class has and seeks to satisfy them. So if you look at CEV<Will and folks similar to Will> you will see a CEV that does take into account the impact of past injustices according to whatever your moral intuitions are.

If we accept that natural selection isn't a moral process and is beyond the reach of God (which doesn't make any sense, but whatever), then it seems really odd to just accept its results as moral even after we've gained the ability to reflect and fix past errors.

Once you eliminate the effects of natural selection - and assorted past genocides - you don't have anything left. It isn't odd to accept whatever morality you happen to have as morality when there isn't anything else. I happen to have my morality because having it helped my ancestors kill their rivals, stay alive and get laid. Take away those influences doesn't leave me with a more pure morality it leaves me with absolutely nothing.