All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger. We ask Allaah to exalt his mention as well as that of his family and all his companions.
According to Islamic principles, the Words of Allaah should be protected from dirty and filthy places, and places of impurities. Allaah Says (what means): {and whoever honours the symbols [i.e. rites] of Allaah, indeed, it is from the piety of hearts.}[Quran 22:32]. Allaah further Says (what means): {…and whoever honours the sacred ordinances of Allaah, it is best for him in the sight of his Lord.}[Quran 22:30]. Therefore, it is not permissible to throw the water on which the Quran was recited into dirty places, like the bathroom and the like, but there is no harm to throw it in a pure place like in the home garden or mixing it with drinking water.
As regards the issue of your mother not benefiting from the water on which Ruqyah was performed, please refer to Fatwa 89628.
Allaah Knows best.