I'm not sure if the facts will bear out your statement about the Church killing more than the Nazi's. No one has a precise number on how many died during the Nazi regime but I have seen/heard estimates of more than 20 million (both direct and indirect).

Church and religion in general have been cause the of many many deaths throughout history and perhaps if you went back far enough in time you might surpass the number from Nazi's

In the same time frame however? Nope the Nazi's were responsible for more deaths in that short time frame than any other movement in history.

The Crusades were one of the worst initiatives by the Church and most scholars agree that the mean average is around 1.7million deaths. A lot for sure, but not close to Nazi numbers.

Add in the Inquisitions, the dark ages, the supression of scientific advancement and the persecution associated with it, the many many wars Church's and different religions that profess to preach love, peace and harmony (only their concepts of love, peace and harmony of course) and the numbers get much closer.

As to why the Church is loved and the Nazi's hated?

Well don't forget, while Hitler was in power, the German's LOVED him. He brought the majority out of poverty, told them they were better than they believed, that they had a destiny, a higher purpose, came from divinity (hmm a lot of this is sounding familiar isn't it) and so forth. If the Nazi's had won the war they would probably be loved as well even today. Only because they lost are they now reviled instead of revered. 

See its simple, those in power shape reality. Hitler's promises fell short and so he is remembered in history as a bad guy.

The Church's on the other hand, still wield immense power, set world wide policies and such and have BILLIONS (including all religions) of followers all over the world who still worship them, believe in better things to come, that they have a purpose, are destined for greatness and will be, if they follow the rules created by MAN (not a divine being), they will be rewarded later in life.

Pretty much the same principles Hitler touted to get the people on his side. One worked, one didn't.

The church is loved by many despite the number of scandals that continue to rock it. Sexual scandals, financial scandals, the hoarding of knowledge in not-so secret archives, the changes of policy (belief in aliens does not preclude a belief in God, there might be other intelligent life out there) albeit slowly they are catching up to the rest of the world. 

They continue to offer the one thing that most people want: Hope

Hope that there is more, hope for a better now, hope for a better then, hope that your life is meaningful, etc.

The Nazi's were loved when they still offered hope, reviled when they didn't

The Church is the same, except they still offer intangible hope to billions of people and so those people are willing to buy a lottery ticket for that hope and pray that the Church can finally deliver on its promises.