Your question is so broad that giving a precise answer is going to be nearly impossible and obviously there will be a lot of generalisation.

First we need to clarify something: violence isn't always violence. Christian vs Muslims was seen as very justified violence and was basically given the green light by the bishop of Rome himself.

What had moral implications where we had Christians vs. Christians, but also here we do see different levels. The more familiar the practices of the faith were, the more moral weight violence had. For example the Byzantine Christians were viewed as less by the Catholics. Later we have a similar dynamic with Protestantism and Catholicism. During the reign of Louis XIV we know that when a protestant army laid siege to a protestant town there were significantly more desertion than when a protestant army laid siege to a catholic town.

So why do you assume that Christians were comfortable with war and violence during that time? Because there was a lot? That's like saying we're comfortable with pollution because there is a lot. Obviously some people care more, some care less. We have accounts of people completely refusing all violence, we have accounts of people committing the most unchristian attrocities.

In addition to that is the simple reality that concepts often don't manage to represent the nuances of reality. Just because you believe in something, like I believe in climate change, doesn't mean that you completely act accordingly. I still drive my car for instance. So some people believed in the act of non-violence in principle but didn't act accordingly.

What probably also played a part is the whole concept of sin. You can be a sinner but it's weighted against your good deeds. Being a sinner in itself isn't that bad if you attone for your sins. A murderer can still be redeemed if he makes up for his crimes. Then we have the whole institution of the purgatory, where the church basically sold quick passes to heaven. We also have accounts of people raiding and pillaging villages because a bishop said it was in gods will. What I am basically trying to say that the Catholic church had a monopoly on morality and absolution and they used it to control society.

To summarize: the peasants probably weren't comfortable with the violence that happened (how much violence there was is hard to tell). However there was nothing they could do about it and accepted it as a part of their lives. Sorry for the very broad answer but it's an extremely unspecific question to answer.