It is not clear that Mary made the decision entirely by herself; at the time, she was in France with her husband King Francis II, and they were both young (in August of 1560, she was 17 and he was 16). Mary's regent, her mother Mary of Guise, had only just died, and their court was dominated by the "Guise faction". The official reply to Parliament was in the name of Francis II, who wrote:
Mais nous trouvons ... que votredite résolution est fort eslongnée de ce que vous devez faire en nostre endroict : ce qui ne nous a pas grandement pleu.
(My translation:) But we find that your said resolution is much removed from what you ought to do in our place, and this has not greatly pleased us.
The records of William Cecil contain a summary of this letter:
FRANCIS II to the ESTATES OF SCOTLAND.
Has heard the message of the Chevalier of St John2. Is very much displeased with their proceedings, and hopes to see them return to the good path which they have left. Will send two noble persons as deputies to assemble the Parliament legitimately. He, for his part, is willing to forget past offences, as he has declared to the Chevalier of St John. - Orleans, 16 Nov. 1560. 3
In any case, the legal issue was the legitimacy of Parliament to pass laws on religion. According to the agreement of 8 July which led to its meeting, any religious matters were to be deferred to a later meeting between Mary and a parliamentary delegation. They were also not meant to take any action against Church estates for the time being - but instead, they did start the process of breaking up large property holdings, regulating tithes, and denying the authority of the Pope or the Crown to make appointments to ecclesiastical office. All of this was part of the package of legislation that Mary and Francis were asked to ratify. It was a huge step for a Parliament that historically had left religious affairs to other authorities.
Other legitimacy concerns related to the procedure and membership of this parliament, as the Protestant faction was able to arrange a particularly strong representation for themselves. This group was strongly in favour of alliance with England instead of France, and was trying to marry the Earl of Arran - Mary's heir - to Elizabeth I, as part of a plan to unite the two crowns under a Protestant. Clearly, this was unacceptable to France and to Mary (it eventually happened with her son James VI). The Archbishop of St Andrews, who was also the Earl of Arran's uncle, requested Francis and Mary to withhold ratification, in the hopes that more moderate Protestants than Knox would then be willing to seek a compromise - some sort of religious tolerance, as opposed to the Protestant absolutism of the Confession. We also know that they were lobbied by Pope Pius IV to stand firmly on the Catholic side, and make no concessions.
Doctrinally, the action of Parliament was held (by Knox) to be founded not on royal authority, but on divine law, making any procedural problems irrelevant. In the same way, the Confession and the First Book of Discipline (also 1560) envisage that the state has no role of governance over the church. The rejection of the 1560 Parliament's acts, founded on legitimacy concerns, is not only a political statement but has a doctrinal dimension, regarding what the relationship between church and state ought to be.
Moreover, the monarch is expected to be faithful to Christian doctrine in the form expounded by Knox, meaning that Mary, for example, could not attend Mass even in private. So it's not a question of whether she would agree that her Protestant subjects could follow the Confession, but more of her denying that everyone in Scotland, including her when she returned, had to abide by it. As a matter of conscience, she was unwilling to resolve the sectarian crisis in the way Knox preferred (everybody becomes Protestant, problem solved), preferring a model where she and others could remain Catholic.
- History of the Scottish Parliament (3 vols). Edinburgh University Press (2004-2010). See especially the chapter by Keith Brown on the Reformation Parliament, at the end of volume 1.
- For more on politics and legitimacy: Le crépuscule de l'Auld Alliance : la légitimité du pouvoir en question entre Écosse, France et Angleterre (1558-1561). Eric Durot. *Histoire, économie et société 27(1):3-46. 2009.
- William Robertson's History of Scotland (1759) contains a brief account of Sandilands getting a frosty reception from the royal couple.
1. Négociations, lettres et pièces diverses relatives au règne de François II, Louis Paris, Paris: Imprimerie Royal, 1841, at p692. Found thanks to the article of Durot (his note 229, on p39)
2. James Sandilands, Lord of Calder, head of the Order of St John of Jerusalem in Scotland, was the official messenger sent by Parliament to Mary and Francis.
3. No. 712 in Calendar of State Papers, Foreign series, Elizabeth vol. 2 (1560-1561). ed. Joseph Stevenson. London: Longmans, Green, Reader and Dyer (1865).