I am not sure what the correct answer is (if the milk is contaminated with thrush) but can offer my experience:
I got painful thrush in the milk ducts after having cracked bleeding nipples and the course of fluconozole cleared it up (stopped pain deep in breasts) my nipples also healed but continued to feel a bit sore and were red for a long time until i eventually found the right cream which cleared it up. Managed to clear thrush of babies bum too (this all took weeks) but to this day he still has it in his mouth (he is 2 and half months old now, we got thrush in the first week!)
However, I am not in pain, and he doesnt seem at all bothered by the small amount of white on his tounge, so I stopped giving him the oral gel. I am confident that now that the latch is good and I dont have cracked nipples I wont get re-infected in the milk ducts, and my nipples arent even sore anymore (perhaps because I am able to keep them dryer now, less feeds,and no more lasinoh? whatever the reason, the thrush from his mouth doesnt seem to be growing on my nipples anymore)
Anyway, (sorry this is getting long) my point is we havent completely eliminated the thrush, but no one is suffering anymore, so I am no so bothered about the re-contamination thing. If you have cracked nipples I definitely would try to totally eliminate the thrush and wouldnt take chances with the expressed milk, because otherwise it will go right back into the ducts, however if you are healed, perhaps its not so necessary.
not sure if that helps at all, but you have my sympathies too - hope it clears up soon!