What if the Scottish Queen had been able to marry John of Austria after the death of Francois II of France? how would that have changed the european politics of the 16th century? could it have saved John's life? could it have saved Scotland?
Elizabeth would have come down on Mary like a hammer if she tried to marry Don John of Austria. Remember also that a) Elizabeth was rather well-disposed toward Mary in the beginning, and less inclined to side with Protestant rebels than almost any of her councilors were, and b) Philip II at this time did not wish to antagonize her, and so would not favored the prospect.
Don John was also a teenage boy at the time you're presumably looking at - he was only 23, IIRC, at Lepanto. Of course he was eligible to marry by the standards of the time, but not yet a commanding figure in his own right. By the time he was, and Philip would support the idea, Mary was already under lock and key in England.
-- Rick