You can't get rid of them but you can change their unit on the general tab using civ3edit. If you change the basic and advanced units from warrior and horseman to worker and settler they should no longer cause a problem. They would then represent friendly tribes wandering around waiting for someone to guide them to the greatness of an established civilization instead of the evil, bloodthirsty, savage raiders they normally are.
Personally I like the bloodthirsty, savage raiders.