Yes. The marriage was considered as unifying the two crowns: even if she had died childless, the terms of the marriage contract called for France (the French royal family) to inherit Scotland, as well as her claim to the English throne. In the same year that the contract was signed, 1558, the Scotland and France gave each other's citizens the same rights as natives. The 1548 Treaty of Haddington had already given France a certain permanent amount of authority over Scottish matters, and Mary Stuart's mother and regent was a daughter of the powerful French Guise family. Many Scots were not quite happy with the extent of French influence in their government, but the intent was essentially to absorb it, turning the Scottish title into the equivalent of the princedom of Wales for England.

But at the same time, you never really know "what would have happened", particularly when it comes to predicting successions, which are fraught with contingency. In the modern world, we can be fairly certain that a) intended heirs will not die suddenly, and b) the pattern of succession will not be seriously changed. In the early modern world, neither was remotely certain. The fact that Elizabeth Tudor became the very successful Elizabeth I of England was incredibly unlikely at the time - her father had to not have multiple sons, her younger brother had to die before he got married and had children, her married older sister had to die without issue, her brother's rearrangement of the succession to omit her had to be dismissed, his chosen heir had to fail to hold onto the throne. In a similar fashion, Francis and Mary could have eventually decided to split the kingdoms apart between two sons, or Scottish nobles could have gained the power to demand the reversal of the treaty and marriage contract in favor of self-government even at the risk of vulnerability to England.