People somtimes feel threatened by others who are different, and reject them unfairly - looking for evidence in The Chrysalids, from the Japanese Internment, and today's society to support this statement.
The internment of Japanese Americans, many of whom were from my hometown, wasn't on the basis of their being "different" and therefore fearsome; it was on the basis of wrongly evaluated ethnic/genetic association with the "enemy." In this "us"/"the other" scenario, the enemy attacking from Japan was real and not "felt." The only parallel in Wyndham's The Chrysalids to this actuality is the enmity expressed by the lady from Sealand to those who were attacking the telepaths. Her enmity was associated with a genetic variance and based upon a real attack.
This is clearly shown in The Chrysalids by the response of the Waknukians to deviants and mutants. Even the fact that they would classify Sophie, a little girl who has one extra toe on either foot, as being a mutant and therefore not a human, shows how threatened they are by difference. You have identified a neat parallel with the Japanese internment.
Looking back at the Japanese Internment, it had no real effect on the war effort or on security other than public opinion; I would question the use of it for that reason alone, even aside from the blatant human-rights violation. Remember also that many young Japanese-Americans volunteered to fight for the U.S. rather than be interred; this speaks to their sense of duty to their adopted country and their sense of self-preservation (not that a war is safer than an internment camp, but at least in war the enemy is known). It is also interesting to note that German-Americans were interred during both World Wars; they do not receive the public attention and sympathy that the Japanese Internment receives today.
It would be nice to think that this kind of prejudice were a thing of the past, but of course it is not. There are religious and ethnic conflicts taking place at the moment all over the world. The Chinese suppress the people of Tibet; ethnic tensions in Africa have led to very bloody conflicts; and I was just reading last night about ethnic conflict in Burma. I have taught many Christian students from Malaysia who have come to the U. S. to be educated because of quotas in the universities there. This list could easily be extended, unfortunately.
Some of the posts above note that many of the people interned were American citizens. I would like to point out that the ones who were not American citizens were not citizens because we had a law prohibiting the naturalization of Asians. Therefore, only Asians born in America could be American citizens. The Issei did not have a choice. This shows that Americans were rejecting people who seemed different long before the war started.
With respect to Japanese internment, fear occasioned by the war led to widespread support for FDR's policy of internment. Many of the people interned were American citizens, some of whose relatives were actually serving in the U.S. Army. They were interned solely because of fears over their background and, ultimately, their appearance. In the the Chrysalids, the inhabitants of Labrador fret over even the least deviation in appearance, even among animals. Those who are different are banished or even killed. In today's society, at least in America, many politicians and other Americans demonize "others," with perhaps the most telling example being the recent fear-mongering surrounding "shariah law."