One of the glaring questions for a discussion of martyrdom is something of the lines of 'what are we to do with those who died in sectarian violence between Christians?' That is: what of those who were executed for being Catholic/Protestant/Anabaptist? In what sense are they martyrs?
There are two obvious ways to analyse this question. First, you could take the traditional view and say that only the martyrs to my particular cause were truly martyrs because only they were dying for the truth. And, in addition, you might seek to take the high moral ground (as Foxe does) and show that Catholics burnt far more heretics than Protestants ever did. As Augustine said, not the suffering but the cause makes the martyr. He wouldn't have the Donatists as martyrs, and was quite happy to set the soldiers on them.
Or, second, you could take the view that in some sense martyrs of every hue were (at least potentially) true martyrs. Now to do this, you have to theorise that both Cranmer and Thomas More were in some sense witnessing to Christ - perhaps imperfectly, but equally validly. This isn't an easy route to follow, because you have clashing beliefs in force.
What won't do is to see the martyrs as merely witnessing against crown/church practices of execution. That is not what the martyrs saw themselves as doing! Take Cranmer for example - I don't think he would have denied Mary the right to execute heretics by burning, even if he would have disputed her criteria for selecting victims. He was quite happy to burn those he thought were heretics after all! Even the more radical reformers (say, the Dutch Mennonites) did not see themselves as dying for some principle like non-violence. They thought they were testifying to Christ.
I guess a third, and more secular, strategy would be to say that the whole martyrdom idea is dangerous when applied to this period because all it does is bolster sectarianism and its potential for violent conflict.
Hmm..