Pope John Paul II delivers most sweeping papal apology ever, repenting for errors of church over last 2,000 years; public act of repentance, woven into liturgy of Mass in St Peter's Basilica, is unprecedented in history of Roman Catholic Church; was carried out despite doubts of many of his own cardinals; Pope says new evangelization in third millennium can take place only after church-wide 'purification of memory;' seven cardinals and bishop, underscoring religious significance of apology, cite during Mass some of key Catholic lapses past and present, including religious intolerance and injustice toward Jews, women, indigenous peoples, immigrants, poor and unborn; photo (M)