I know, thats not what you asked for, but i would not let him take that prejudice against humanis as a negative quality. He may hate them as a background option though without getting any BP for that. I would assume that most of mankind hates humanis. Its like publicly stating that criminals belong to jail, or criminals are bad - of course they are, its a common opinion and not a prejudice. In an argument with humanis, because of his attitude, most people will be on his side, while with a real prejudice he should have most people against him!
For the background stuff, let him make some suggestions, it was his idea after all, or he should take something else.
Also you don't have to create it in the beginning, make it up as the runs go by. And if at some point he gets his memory back and loses the negative quality, make him pay with karma for it. And until then it should be played as a negative quality. Most of the time, those players are just too lazy to create their own background, especially if they don't have any suggestions themselves. He should not get rewarded for that.