Hi C. -
I'm sorry to hear that your daughter had the thrush. I hope she's better now.
While I'm sure you'll receive lots of advice on weaning her gently from her pacifier, what worked for both of my older children was making them quit cold turkey. Actually, my mother took on this challenge that lasted a grueling week, but in that span of time, she managed to completely wean them both at age one. My kids were a little too young at that age to reason with them when it came to weaning, however, your daughter is older, so it may work. Telling her that big girls don't need their pacifiers might appeal to her growing independence, or it may not...it really depends on your daughter. Also, from a more pragmatic standpoint, you may want to just cut the nipple so that it deflates and she can't suck it anymore. That seems to work for many kids.
In any case, bless you and your daughter on this endeavor. If can you break her of this habit, it will be yet another great milestone.