I have not read either of the biographies which you mention, although I would hope to do so when I can. I agree with you that Mary's attitude to Elizabeth was quite forebearing given what Mary herself had been through (not that this was Elizabeth's fault), and the fact that Elizabeth was undoubtedly involved in activity which was aimed at undermining Mary's position. I would like to think that their being buried together at the end was a recognition by Elizabeth of the difficulties of Mary's position, and some of her virtues.
I also agree that many of the deaths in the Marian persecution of heretics were driven by those around Mary rather than by the Queen herself. Many of the Bishops in the Church were determined to try and root out protestantism, and we need to remember that there had been earlier examples of this from those now thought of as saintly, eg Sir Thomas More, who was an enthusiastic persecuter of heretics.
I would however like to take slight issue with your view of Henry VIII. No-one can deny that his attitude to his wives was the very opposite of ideal, and he was a manipulative man who ruled his court through the 'divide and conquer' tactic of setting factions against each other. But in one respect, his desire for a male heir, I don't think he should be seen as anything exceptional. Many countries, eg France, had the Salic law which actually forbade any female monarch; England did not, but its previous experience with the Empress Matilda had done nothing to remove the prejudice that a female heir would lead only to civil war. In the event, Mary reacted strongly and breavely when her succession to Edward VI was threatened by Dudley but there was no guarantee that a woman would find it possible to rule, and Mary had the advantage that Henry had placed her in line of succession and this still carried more weight than Edward's attempts to change it. The problems experienced by Mary Queen of Scots, eventually ejected from her own country by the nobility, are an example of what could happen to a woman ruler in the 16th century. There was also the problem of marriage, and Mary's marriage to Philip of Spain, who was refused the Crown by the English Parliament, and Elizabeth's subsequent refusal to marry, show the problems that could cause for a Queen in a man's world.