With all the respect I might have for your opinion, superstitions and irrational cruelty (especially in Europe) was pretty common. Besides, being a part of a religion doesn't make you responsible for all of the actions other people in that religion did commit — Jesus taught us love and compassion, and the way some people interpret these words is up to them.
You don't ban nuclear energy, despite it was used twice as the most powerful weapon in the human history, and being prophecied as the end of human race. I know that it's slightly different topic, but still you may connect dots the very same way.
Misinterpretetations, superstitions, and much more were, I may repeat it once more, common in past.
And even now, in age of internet, stupidity lives on, from believers in weird spirit grannies running in Japanese road tunnels at 100 mph, to fanatics that insist on the fact that diet with absolutely no animal products is healthier than perfectly balanced one.