Well now we know why few people visit the Hakurei shrine

From The Call of Duty Wikia: No Russian - Regional Differences

In Japan and Germany, if the player kills a civilian, the game will restart from the last checkpoint with the "You killed a civilian!" message.
In the Japanese version, Makarov's line, "Remember, no Russian" is mistranslated as "Kill them, they are Russians." This was criticized as the plot of the game was centered around the terrorist's motivations and as a result the goof caused some confusion.

See also these pixpedia(JP) and Nicopedia articles.