But Thomas disappearing was because of Rumple though, wasn’t it? I mean, since Ella got him back when her deal with Rumple was honoured (or at least another deal made instead) I figured it was the fact that she hadn’t honoured the deal that caused him to disappear, not the quill thing.
Also, the fairies get their magic from the dust and I think the dust could be considered already paid for with all the work the dwarves put into it. Work is a form of payment after all.
I do agree though that probably all forms of magic in FTL come at some sort of a price, even Regina had to kill her father in order to make the curse work.