Don't do anything to the milk!! The milk does not have the thrush, the thrush is in your babies mouth and on you - there is no need to worry about the milk and the milk is totally fine. I EP'd and had thrush many times (from antibiotic overgrowth - long story) the best thing you can do is be proactive about your nipples. Sterilize your horns after every pump(the microwave sterilize bags make this faster) change your nursing bra after you pump, change your shirt if you leaked on it, air dry your nipples completely before covering them. Wash your nursing tops together and on the hotest water possible (some people boil them).
Also, don't use any lanolin on your nipples, that feeds yeast overgrowth and if you are prone to thrush can help you have recurrent thrush. If you need a cream there is a triple antibiotic cream you can make for your nipples from over the counter stuff.
DS never really showed signs of thrush so I didn't treat him, I just took the antibiotics myself (they weren't the ones that caused my yeast overgrowth by the way - I had a lot of BFing issues...) As soon as I had 24hrs on the drugs I felt better.
Feel better soon!! But know your milk is totally fine. Your milk DOES NOT have the infection.