For anyone interested in the truth, there is a book The Pius Wars, published in 2004 or 2005 which includes an exhaustive 180-page annotated bibliography of this controversy by Bill Doino and about eleven chapters by various authors, Catholic and Jewish and otherwise who have risen to the defense of Pius XII before a generation who do not remember him and his work.
The controversy did not exist at the time of Pius XII's death in 1958. Pius XII was well aware of Angelo Roncalli's (the future John XXIII) efforts on behalf of Jews including the manufacture of passports and baptismal certificates and the establishment of a cooperating underground railroad that sent Jews in safety from Europe to North Africa through Spain.
The controversy began with the early 1960s publication of a play The Deputy by one Rolf Hochhuth attacking Pius XII's character and portraying him as a cold-blooded anti-Semite in league with the Third Reich. Somehow, these slanders had not been the view of those familiar with the facts and the historians and objective observers and Israeli political leaders (many of whom were atheists or agnostics as secular liberals).
As a conservative Roman Catholic, I would let the reputation of Pope Pius XII (who will, despite his enemies' efforts, become Pope Saint Pius XII just as Pope Blessed John XXIII will be canonized as Pope St. John XXIII) ride on such sources as Albert Einstein who effusively thanked Pius XII for his efforts against the Holocaust, Golda Meir who eulogized Pius XII in her capacity as Israel's UN Ambassador, Israeli diplomat Pinchas Lapide who wrote an entire book on the subject as a contemporary observer of Pius XII work to save Jews and Benjamin Gilbert, a noted Jewish historian and biographer and Oxford professor who has written repeatedly and in scholarly depth on the subject.
What were Hochhuth's credentials to examine in an effort to discredit the WWII resistance of Pope Pius XII to the Nazis and to the Holocaust? Hochhuth's father was a WWII SS officer loyal to Hitler and the Third Reich. Hochhuth was, during the Third Reich, a member of Hitler Youth. After the war, he became a Marxist and in that capacity was an enemy of all things Catholic. Those who perpetuate Hochhuth's myths include a substantial number of leftist Kumbaya pseudoCatholics like Garry Wills who want to neuter the moral authority of the Roman Catholic Church and its Teaching Magisterium on matters of personal and familial morality, water down the liturgies (including the Novus Ordo Mass) and practices of the Church which carry out the mission of the Church.
What Pius XII's enemies within want is Unitarianism/Universalism practiced within formerly "Catholic" parishes and some of them find even that too restrictive of their desire to follow the heresy of the week or agnosticism or atheism with tax deductions and without Vatican interference and call it "Catholicism." By and large they want a Catholic Church relentlessly advancing the social and economic and foreign policy of the barking moonbat left and stripped of anything actually Catholic. What would they not do to see a Pope Howard Dean???? Are you broad enough and open-minded enough or are you one of those narrow-minded moralist bigots who resist (all genuflect, now) CHANGE????
Finally, the New York Times, hardly a house organ of Roman Catholicism or of Western Civilization for that matter, editorialized in 1942, after a stinging anti-Nazi Christmas radio broadcast by Pope Pius XII that the lights had gone out all over the continent of Europe until only one candle remained and that candle was Pius XII's Vatican resisting Nazism.
If Pius is to be judged guilty for not doing enough to prevent the killing of innocent Jews, how can they escape being charged as guilty for not doing enough to prevent the slaughter of the innocent unborn, many of whom are Jews.
There's also a bit of controversy about the writings mentioned in the thread-head post. Some folks question whether Roncalli was writing for 'more than one' audience--meaning that he could have known that his letters were being reviewed by Nazi censors prior to dispatch to Rome.