First of all let us discuss why people make accusations against the Church of the Middle Ages. The reason we see these accusations most often is to besmirch the Church in such a way that it is somehow evil and not the Church authorized by Christ to have all authority by God on earth. These same people believe that the true Church is free from sinners and that those within the Church cannot make errors or even are evil lest all credibility of the Church is destroyed if sinners are found. So no matter how hard one tries to besmirch the Church still remains based on the veracity of Christ and not on the veracity of those within the Church who sin. The commission of the Church remains true despite the errors and evil within individual sinners.
Second of all we should examine the time and the culture, not only during the Middle ages but the culture that prevailed until just a few hundred years ago of attacking those of a different religious practices. I agree with the questioner that the Crusades are different from the inquisitions as the first was a defensive action and the latter was offensive. Among the religious there were some atrocious events taking place of which the scope of these atrocities have often been greatly exaggerated. Among the Catholics there were the inquisitions and among the Protestants there were the witch trials. Actually in the latter more people were executed. Among the Protestants there were the abuses in Geneva by Calvin who was called the butcher of Geneva for trying to establish a theocracy by murdering his opposition. Then there was the Three Hundred Years War in which both Christian groups were equally blood thirsty. To Catholics such attacks against the Church are ridiculous in that we know that not all within the Church are saints. Even St. Peter denied Christ three times yet the Church maintains its veracity not on the saintliness of men but on the perfection of Christ who founded the Church. Some men among the faithful will always be sinners and some in a most egregious way.
The truth is that there existed a culture of death in the Middle Ages that continued through the early Reformation where people felt justified in punishing heresy in a most cruel and brutal way as seen from modern culture. Ecclesiastical power was used to the extent it had influence to remove perceived heresy from society. Luther, Zwingli and Calvin are just as guilty, and in some cases more so, than Catholics. But the Church is innocent as it is in Christ while not all that those within the Church are innocent and have actually succumbed to the worldly culture of the time and created a stumbling block to those looking to the Church for moral direction but the sinners within the Church do not detract from the God given authority and divine inspiration that is only present within Christ's Church. God bless!