if they want to restore themselves, and the respect the world once had for them, the Cathoic church is going to have to do a lot of restructuring and cracking down.
the cathloic ministers I've met are usually good guys and their congragations are actually a force for good, but I think corruption sets in at the mid levels somewhere, and it's crippled their image. I heard of some groups of ministers starting to wonder about splitting off.
old "Mother Church" has lost moral authority when they became "the harlot of rome" (if you listen to calvinists) sometime during the early rennisance.
and to the list of percicutions, it was a bloody brutal time that the church inherited from the fallen romans, and every warlord used their faith to justify slauthering and trying to carve out a kingdom. so part of it was the bloody times, part that the church was kind of "politics of faith." That jesus would not have wanted, and that in-fact had him percuted and crusified in the first place.
People blame the church for it's brutality, but it's opposition was just as brutal especally in the early middle ages, the Papacy was just more organized, and could throw it's weight behind the warlords it liked.
I'm not painting it as a hero, or as the great power it imagines itself as, I just think they are blamed for all religious brutality in the middle ages, which is actually unfair... most of the time it was the local rulers who actually held their own witch trials.
The crusades were brutal of course, but their brutality cannot be blamed on the church alone, partly the result of a kind of peace in europe, you suddenly had millions of unemployed professional soldiers, knights, and generals. When the Byzantine emperor requested aid against the islamic armies in the east, the Pope used the local sultan's refusal to allow pilgrims in to the holy city as a way to get all those guys with swords out of europe. and hey if they take a few cities for the church... that'd be just fine...
When the man leading the first crusade lost his wife, he suddenly became impoverished, losing all ties to her wealthy family back home. exausted, hungry, overheated, and now dirt poor... but with an army of professional warriors eager and chomping at the bit for battle, what would you do? the brutality he started upon the people of the middle east in taking their wealth and land started a cycle of slaughter on both sides that only ended when Richard and Saladin agreed to end the cycle of slaughter.
see it's far more complex then "the church sent a lot of guys to kill muslims for having another religon"
and let's not forget the inquisition, a blight on the church if ever there was one... though the office of the inquisition was brutal, their real power was whipping crowds up into a frenzy, and using it to attack anyone suspected of heresy.
the worst branch of the inquisiton was the Spanish, this is because when the blood started to rise, the papacy could not stop them. The Spanish Inquisition answered only to the Spanish Crown, the pope actually had no say in their actions. though I'm guessing it would have still been brutal, but they would have stopped much earlier...
nothing is simple...
but Callie is right, they have marganlized their on flock over the years by being involved in such things, and now the scandals the church is 100% guilty