I once heard a piece of wisdom that went like this: We look at the medieval knights of those ages and see barbarity or cruelty in the plundering, rapes and killiing of innocents that occurred. Although one may truly wonder what these knights would equally have thought about concepts like saturation bombing, landmines that remain in the ground after the war, or even nuclear weapons.
I think the world is far more barbarous today than it was then.
The church as a teaching authority cannot be faulted, but as a corporate entity it most certainly can. Its members really did, and are doing now, and will for years to come, commit sins that caused harm to their neighbour. The same is also true of non-christians who have not come to the grace to be made perfect from this sinful state.
I think God could have been punishing the jews by ways of these pograms and acts of violence, although that does not necessarily mean the people who perpetrated this themselves are guiltless, or that doing so was not itself a sin on their part (consider the Chaldeans who were used to punish Israel who committed a sin themselves in their plundering and destruction, even if God used this plundering and destruction to chastise His people, Habakkuk 1:13 Thou who art of purer eyes than to behold evil and canst not look on wrong, why dost thou look on faithless men, and art silent when the wicked swallows up the man more righteous than he?).
The papacy never supported (openly, or in its official capacity as an institution that is, apart from whatever personal views of the popes) the kind of local violence that often occurred against the Jews all around christendom, although it did support placing jews into ghettos, forcing them to be publicly identified, and subject to a number of restrictions that may fit under the things that the church now gives apology for in regard to wrongs committed against non-believers. The best example of this I know: Pope Paul IV’s bull
Cum Nimis Absurdum, which is a set of rules for Jews in the Papal states in the 16th century that includes what I mention above. Here is a link if interested:
en.wikipedia.org/wiki/Cum_nimis_absurdum
I think we also often forget that the crusades, that had church support, were not meant to be crusades against Islam (even though this was often what they were seen as) but rather as crusades to supposedly secure the holy land and the protection of pilgrims… the fact that it turned into an event whereby things occurred like when the entire population of Jerusalem (Muslim, Jew… and Christian!) was completely slaughtered by European knights who looted everything they could was not what had been idealized in its mission.
But what is an even greater atrocity than this, is not the crusades that occurred in the Holy Land, but rather the crusades by which the western hemisphere was conquered by Spanish and Portuguese armed men. Now that was truly genocide, for the Spanish even denied that their victims were fully human or possessing reason. Even though they had given the land to Spain the papacy condemned it by how it was practiced.