Pearl was the Wall Street Journal correspondent kidnapped and beheaded while investigating links between Pakistani militants and suspected shoe bomber Richard Reid.
His dismembered body was found four months later in a shallow grave in Karachi.
The open letter from the family came after Vice President Dick Cheney mentioned Pearl in a campaign speech where he lambasted Democratic candidate Sen. John Kerry's calls for a "more sensitive" war on terror.
"The men who beheaded Daniel Pearl and Paul Johnson will not be impressed by our sensitivity," said Cheney.
Johnson was a U.S. citizen beheaded by abductors in Saudi Arabia in June.
The Pearl family statement said: "We would like him to be remembered for what he was in his life, a passionate American and humanist who rose above political, religious and cultural divisions, and used his pen ... to connect people of all backgrounds."