nilを代入するだけだよ
print関数を例にすると

lua_State *L=luaL_newstate(L);
//luaL_dostring(L,"print('hello')"); //ng
luaL_openlibs(L);
luaL_dostring(L,"print('hello')"); //ok
luaL_dostring(L,"print=nil");
//luaL_dostring(L,"print('hello')"); //ng
lua_close(L);