"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.

yes you can say that, but its a little weird so just saying thank you is better.