I'm beginning to think that the Blue Fairy might know more about why the Black Fairy's heart darkened then she's admitting to.
We know that Blue threatened to take Nova's wings if she went off with Dreamy, what if either the Black Fairy was given the same ultimatum in regards to Malcolm/Pan but ignored it or Blue didn't find out out the affair/relationship/whatever it was until the Black Fairy was already pregnant. If the Black Fairy was pregnant when Blue found out then losing her wings wouldn't necessarily be much of a threat. If Blue really is that against Fairys interacting/fraternising with humans/non-Fairys in any way outside of their official duties it's possible that she stole Rumple from the Black Fairy as some kind of 'punishment' and made sure that the Black Fairy couldn't find him. Loosing her son then resulted in the Black Fairy having some kind of mental break down and kidnapping children in an attempt to find her own son (which in turn resulted in her heart darkening and her actions becoming worse as she became more mentally unstable). Alternatively she could've turned to dark magic to try and find her son when light magic/fairy magic failed her and her constant usage of dark magic corrupted her and darkened her heart.
Then, by the time that Rumple summons her in 'Changelings' she's so far gone that part of her genuinely believes that she chose to give up her son/it's less painful for her to make herself believe that then to confront the truth.
It would also explain why she resides in a realm where that the Blue Fairy can't find/access and why time doesn't really work there etc.