The Great Seal does not belong to any special group – past or present, covert or overt. It is an original American symbol created in 1782.
Of course, the perception of a symbol's meaning can change. Look what happened to the swastika – an ancient symbol of well-being – after the Nazis started using it. That's why it's crucial for Americans to honor and protect their seal (as they do their flag) and not let it be commandeered by those who distort its meaning by using it as a logo to promote their paranoia.