I think what everyone's forgetting here is that England hadn't had a queen yet - except Empress Matilda (and look how that turned out). They hated Marguerite d'Anjou almost to a man, but supported her husband, the rightful king.
Also, while Marguerite married EoW to Anne Neville, she herself would've viewed it as a mésalliance and would likely have tried to annul it as soon as the Lancastrians were firmly established back on the throne - unless of course Anne had produced an heir in the meantime.
Again, England's going to be reluctant to accept a reigning queen, when there is a young and energetic legitimate male-line descendant of Edward III available.
As to any children of her loins, it will either be a case of Henry VI (if lucid enough when he dies) will pass the crown directly onto the eldest of her son/s, rather than allow a queen to rule England. MoA might have different opinions of her daughter's capabilities and consider her as the rightful queen of England ahead of her son.
And no one is making any guesses as to the personality of Queen Catherine/Margaret. Her brother has almost continuously been portrayed as a psychopath since before Shakespeare's day. And MoA is regarded as a 'she-wolf'. So, no prizes as to how history might vilify the lady.