Fair question, Dr. Brennan.
No, the Catholic Church does not commemorate the Marian martyrs as Catholic saints, because Catholic martyrdom is not simply “death at Catholic hands,” but a witness unto death to the Catholic faith. Though I suspect you know this and are making a larger point.
But that does not mean Catholics should defend their executions. Burning Protestants alive was tragic, cruel, and indefensible. As a Catholic, I can mourn Hugh Latimer, Nicholas Ridley, Thomas Cranmer, and the others as fellow baptized Christians while still disagreeing with their theology. Failing to mourn such deaths would itself be contrary to Christian charity. Catholics are obligated to pray for the deceased, and Catholic teaching does not claim that every non-Catholic is damned. Those outside full visible communion with the Catholic Church can be saved by the grace of God, even if we believe the fullness of truth subsists in the Catholic Church.
I do feel that remembering Catholic martyrs should not become a "tribal scorekeeping tactic" so to speak. Rather it should lead all Christians to repent of an age when the sword was used in the service of doctrine.
And I would also encourage Catholics not to respond by simply pointing to Protestant-led persecutions, such as the executions of the Forty Martyrs of England and Wales, merely to say, “See, Protestants were just as bad.” That may be historically relevant, but it should not be used to excuse Catholic sins.
I feel the better response is this: Catholics should acknowledge Catholic wrongdoing honestly, Protestants should acknowledge Protestant wrongdoing honestly, and all Christians should reject the idea that coercion and execution are proper tools for defending the Gospel.
Ok, lol Steel Man is stepping down form his theological soapbox now.