"Thank you for your generous discount."
(많이) 할인해 주셔서 감사합니다 or 깎아 주셔서 감사합니다. (깎다: cut/shave something)
There is also "잘 해 주셔서 고맙습니다", although it doesn't mention "discount".
잘 해 주다 is "treat someone nicely", "give a good deal/treatment/care", etc.
It is a little vague so you can use it broadly, including when you received a good deal.
But people don't say these things much after a simple transaction.
In most cases saying 감사합니다 is enough.