Because things changed. Margaret was destined to be the second wife of a much older King who had already heirs so a match of low to moderate value. Now Margaret’s still very young son isTHE KING of England, something on which nobody in Paris was counting on when Margaret married.
You're choosing to ignore the fact that Margaret's influence over her son is about to end, as boys were removed from their mother's households in late childhood. The marriage of Edward and Isabella in OTL was meant to give the French crown influence at the English court for an entire reign. They simply won't have that without having a French woman as queen of England.
There is a real world parallel to this in the reign of Henry VI. That Henry was Charles VII's nephew is never at any point considered a diplomatic advantage for either side. When the English wanted peace and the French wanted influence at the English court, both sides sought a marriage. The English wanted one of Charles's daughters -- AKA one of Henry's own first cousins. Charles's objection to this was not the closeness of their relation, but that such a union would strengthen the English claim to the French crown. There is no English claim to the French throne in ATL, so that is not a concern here.
We know with the benefit of hindsight that neither England nor France were in a position for war. It's doubtful either of them understood how weak the other was at this particular moment, as there is a great deal of historical analysis that shows English and French diplomats were often ignorant of the political complexities of each others' kingdoms.
As I said earlier, I don't think a Thomas-Isabella match is a lock, and I could be convinced that another marriage makes more sense in ATL, but this particular line of argument is not very persuasive.