The universe accounts for everything. When the universe detects something (Squall travelling through time) that's occured out of no where in the past, it corrects the course by making Cid and Matron destined to be together beforehand.
So because Squall went back in time to after they were married, the universe made sure they were already married?
And it did this... why?
This is an infalsifiable theory, Serapy.