"Is it wrong to pray that God blesses Pope Francis with martyrdom?" Quite a profound question; yes? The best answer would be, "it depends on what your motivation is". If you are motivated by a desire to be rid of him, then yes, that would be wrong (and sinful). If your desire is for him to be granted a grace that helps us all to grow closer to God and commit ourselves to serving Him more deeply, then it would not be wrong.
Given the current climate of things coming out of the Vatican, it is really, really, really hard (I know and understand) to have a pure motivation in something like this. Yet, we all must remember that God chooses the trials He wants us to go through. If Pope Francis is a trial for you, then God chose it. He wants you to endure this, and learn from it, so that you can teach future generations what faithfulness is.
Pray for Pope Francis, yes. Pray for him to be penitent of his sins; pray for him to lead us rightly; pray for him to know (fully and accurately) what the Catholic faith is, so that he can speak the truth to all. Above all pray that what you do now can be remembered in future generations as a humble and grateful stand for the truth.