You haven't screwed anything up, and everything you've done sounds perfectly reasonable to me. Your daughter said she wanted to give up the paci, you went with her wishes, and now out of the blue she's changed her mind, which isn't anything you could have anticipated. (Also, I don't think this is a 'dire warning against the folly of introducing a pacifier' at all, any more than the experience of parents whose children don't want to give up bedsharing is an argument against bedsharing! I think it's pretty silly just to shove a paci in a baby's mouth willy-nilly, but if a baby is hard to settle or clearly wants more sucking time than you can give them otherwise then I think it's completely reasonable to try a paci. Sometimes we try so hard to avoid potential problems down the line that we end up causing more difficulty for ourselves in the short term.)
It's interesting that she said it was hurting her mouth - haven't heard of a child complaining of that before, and it makes me wonder whether perhaps she had a mouth ulcer or some such that was bothering her, and blamed it on the paci? If that's cleared up, it would explain why she suddenly wants the paci back.
As to what to do about it... Years back, when my own son was three and I was looking for an excuse not to have to give up his dummy (the British term), I looked on Pubmed and found a paper saying that continued use of dummies after 3 was associated with more malformations of the teeth later on (whereas using them before 3 seemed to be fine for teeth). So 3 is actually a good age to be giving up, from the dental point of view (and it's not actually correct to say that there's no reason to give up).
From your daughter's point of view, however, I can see it would be rough to think you'd just relinquished something important to you temporarily and to find suddenly that you weren't being allowed to have it again at all. So perhaps the way to go would be to agree that she can have it now, but, at the same time, to insist that she has to set a date to give it up in the future, and then to work actively towards preparing for that.