Probably not, and she would've wound up as queen of Castile in this scenario - like her older and younger sisters were supposed to be.
As to the potential of Edward II having kids by Margaret, she'd presumably hit puberty around 1294/1295 (11/12yo), and it's not impossible that she would be under pressure to have children sooner rather than later. So, I'd say 1297/8 (as cruel as it sounds, for reasons of politics, if nothing more) as the earliest Maggie is likely to find herself with child.
Now, can she be deposed à la Mary Stuart? Sure, why not. One problem, you're deposing her - whose husband is either the king of England/prince of Wales (depending on when this deposition happens) - in favour of a baby/child who is going to succeed to that throne in Westminster in due course. Sure, you can do something dodgy with the succession and split the crowns between a first and second child, but as long as Edward Longshanks is alive, I have a feeling the Scots are gonna be leery of doing anything. They might also be aware, if you depose Queen Maggie (and her English children), that you're opening a whole can of worms. You have King Edward II murdered à la Darnley, you're opening a can of worms. And that can of worms is called "English reaction". Edward I won't stand by and watch his son be dethroned (if
Braveheart is correct in portraying the relationship between Longshanks and his son), likewise Edward II is proud/vain enough that he would
certainly have a reaction to it. Edward II is murdered by Scots, the English will have a field day with that and it would probably lead to war (or threats of war) in the wild and woolly north.
@REICHFURST had a
TL, sadly dormant, on this exact premise (the Maid of Norway marrying Edward II).