1. Most of Christ's commands are harder than their alternative. Being generous is more difficult than being selfish. Being pure is much harder than lusting after our desires. Being faithful to Christ is much harder than becoming a martyr. But just as the fact that selfish, lustful, and unfaithful Christians have walked the earth don't disprove Christ's ethic, so it would be for Bonhoeffer's example of throwing off pacifism in the face of great evil. A Christian denying Christ in the face of torture and death no more disproves Christ than Bonhoeffer throwing off pacifism in the face of a man like Hitler. 

2. Even if Bonhoeffer gave up on the pacifistic ideology, we could find a number of individuals who clung to non-violence in the face of great evil (a good starting list can be found in this article). 

3. I'm not familiar with the evidence, so I will emphasize that you must look into this further if it is of interest. Some believe (as in this article) that Bonhoeffer did not actually throw off his pacifistic ideology at the end of his life. They use documentation of his arrest, his own writings, and other evidence to make the case that Bonhoeffer held onto his pacifistic ideology until the end. If he did, that certainly doesn't prove pacifism right, but it would help to at least undercut this argument a little more. 

Jesus Christ was certainly unique, as was the role he fulfilled. It is perfectly fair to be cautious about being overly prescriptive. We could turn many aspects of Christ's life which shouldn't be prescriptive into prescriptions. We could say that because Christ was 30 when he began his ministry, we should require all who desire to work in ministry to be at least thirty years of age. We could say that because Christ was an itinerant teacher, we should likewise be itinerant. We could over spiritualize and over prescribe directives if we attempt to imitate Christ's life in total. The question here, then, is should non-violence be prescriptive, or was it just an optional mode Christ used for his ministry, and/or a specific role he needed to fulfill as the savior of the world?

It seems hard to imagine that the enemy love of Christ was a means taken on by Christ only to fulfill his messianic role. Am I to believe that enemy love is a role of Christ, and not a characteristic of God which we are to emulate? Isn't the notion of enemy love vital to my salvation? Didn't Christ die for me while I was his enemy, while I was far off, and before I loved him? Enemy love is vital to soteriology, and it is vital to understanding the character of God. To say that this is simply a role God uses just doesn't fit with the God of the Bible as revealed through Jesus Christ.

Beyond that, of the relatively few specifics Christ gave to his followers, two things we see pop up over and over in the gospels, and continue throughout the epistles, is the promise that we Christians are to bear our crosses and expect persecution. I love the way John Howard Yoder describes this expectation for the cross and persecution. 

Bearing our cross is simply unrelenting obedience to God in the face of seemingly overwhelming odds, and the temptation to use other means. Christ refused religious rule, political rule, and military rule at the outset of his ministry when the Devil tempted him in these three ways. He refused to be crowned king by the poor when he provided them bread, he refused rule from the religious on Palm Sunday and when he taught in the temple, and he refused military rule when he withheld the legions of angels he could have called to defeat Rome on the night of his betrayal. The harshest words Jesus ever had for his disciples was when he linked Peter with Satan. And why did Jesus tell Peter and Satan to stand aside? Because they declared that God's means of suffering were not valid means to use in the world. The lesson wasn't learned, however, as Peter more forcefully attempted to circumvent God's means at the height of Christ's temptation to do the same. Peter used his sword to swipe at Christ's accusers, as Jesus looked his enemy the Devil (who had indwelt Judas) in the eyes and chose love, healing, and submission to God's foolishness. Jesus saved his condemnation not for Judas or his armed band, but for Peter, when he said, "No more of this!" All who live by the sword will die by it. 

Christians have turned the bearing of our crosses into something we rarely see (at least in the West), and something we absolutely try to avoid. But that doesn't seem like something that is a possibility for Christians, if Jesus has made bearing a cross an expectation for following him. As Yoder points out, bearing our cross is not something we wait around for. It's something purposeful. It's pursuing the means of God without regard for the powers of society. We take the cross upon ourselves. We purpose it. We don't wait for it. Jesus also shows us that our cross is not quietism or insurrection. You can't say that Christ was passive. If he was, of what interest would he have been to the rulers of his day? But at the same time, he wasn't an insurrectionist. He did not attack the powers with force. The cross is also not the Golden Rule. Jesus doesn't just tell us to do to others as we'd have done to us, but to follow his example. The cross of Christ 

The way of Jesus in his submission to God and his means of love in the face of evident defeat is apparent. We're not talking about trivial prescriptions here. We're talking about the core of Christ's message and the means that are meant for his Kingdom. Christ's death on the cross wasn't just a transaction. Jesus didn't come only to die on the cross. He came to exemplify what obedience to God looks like in the face of seemingly insurmountable powers, and he tells us that we have the same lot.

I'm sure this explanation is far too short to be convincing, but hopefully it piques your interest. I highly recommend John Howard Yoder's book "The Politics of Jesus," where he makes a case for Christ's example here to be followed.