Hmmm...my suggestion would be that maybe you should keep her and the puppies completely separated for now. I don't think it was the most ideal situation to bring a new dog in around such little ones. Lol...seems you may have gotten in over your head bringing in a new, obviously dominant, female to an environment where you already have your hands full caring for two litters?
In any case, if she is loving otherwise and is just not getting along with the dogs you already have, I would not think the logical choice would be to have her put down, but maybe rather have her put in another home with someone who has more time and patience to give her the attention she needs to adapt to a new home.
Good Luck!