Accidental Aesop: The villagers do not take kindly to outsiders, to the point that they're worse than the disgusted visitors are. This brings an unintentional "discrimination is a two-way street" message to the story.
"Obed he kinder takes charge an' says things is goin' to be changed ... others'll worship with us at meetin'-time, an' sarten haouses hez got to entertin guests. . ."
Harsher in Hindsight: From the story (keep in mind this was written 70 years before Gitmo and the War on Terror and, more disturbing, only several years before the Holocaust and the internment of Japanese-Americans):
"Keener news-followers, however, wondered at the prodigious number of arrests, the abnormally large force of men used in making them, and the secrecy surrounding the disposal of the prisoners. No trials, or even definite charges were reported; nor were any of the captives seen thereafter in the regular gaols of the nation. There were vague statements about disease and concentration camps, and later about dispersal in various naval and military prisons, but nothing positive ever developed. Innsmouth itself was left almost depopulated, and it is even now only beginning to show signs of a sluggishly revived existence."
Lovecraft was likely aware of the Palmer Raids just after WWI, in which the federal government arrested and deported hundreds of foreign-born radicals without due process.
Nausea Fuel: They interbred with slimy, ugly fish-frogs from the Stygian depths of the sea!
The air of Innsmouth is usually described as having a pungent stench of rotting fish.