Your story is going really well
Instead of changing it all, you could have her used as a surrogate broodmare. So the foal wont have any of her genetic material. They do it often with racers, where they take the best mare's and stally's embryo, but emplant it in another mare, so the good mare can still race.
And a good thing could be, when the foal is born, the mare senses it is not her baby, even though it came from her and has her smell. Just and idea ;)