Can you get to see a lactation consultant? Or see another doctor. oR YOUR mchn. If you do have thrush (and it sounds to me like you do, though I'm not a doctor!!) it is easily fixed. You just need some oral thrush treatment to put on your nipples, like daktarin gel. Also letting them 'air' (ie not wearing a bra for a while each day) and letting some sun onto them will help, as will natural yogurt (eating it and putting it onto your nipples). DS2 and I have thrush now and it can be very resilient, but essentially fairly easily fixed with some persistence.
TBH, I don't see that one bottle would make bub reject you, though it can. But for you to use a bottle once a day so you can get some relief is better than you persevering to a point and then saying stuff it and deciding you can't do it anymore because of the pain. Try to find someone else to give you advice, your doctor sounds like he has no idea! Good luck. I know how painful it can get