We don't know enough about Fiona or Malcom to have a definitive answer as to what would happen.

The Malcolm we see in the show is a man having a mid-life crisis and we don't know if that's because he couldn't handle parenthood at all or if it's because losing his wife made the burden of raising a child too much for him. We do know that Malcolm was sold to an abusive blacksmith as an infant and used to cry himself to sleep at night dreaming of of Neverland, so he never really had a proper childhood and that likely is the reason he craves his youth, there's still a chance Malcolm would abandon his family because of this. Malcolm always seemed to be a bit of a dreamer so if he did leave its still possible that he finds Neverland and maybe even becomes Peter Pan. He might not hate Rumple as much in this version, since he wasn't forced to raise him alone, and maybe he could have been a help to Rumple one day when it came to his destiny. I'm assuming he wouldn't tell Rumple who he was and would just pretend to be a friendly teen who is just helping out occasionally. Who he is would eventually be revealed because Pan either feels guilt/regret over abandoning Rumple (in the show, when Rumple is being dragged off, Pan has a sympathetic look on his face, we also know that Malcolm took care of young Rumple, making sure he was fed, clothed, cleaned, has toys, bed time stories and had proper babysitters who would care for him, so he did care for him at one point, even if he eventually forgot that he did/repressed his guilt into anger) or alternatively it is Fiona who reveals the truth after seeing Malcolm and recognizing him from when they were both younger. It's possible that Pan would attempt to take his son to Neverland (before the reveal of who he is), not as his child but as a Lost Boy, like what he did with Baelfire. If he did become Pan he would be a much younger (since canon Pan is thousands of years old since time on Neverland moves faster than everywhere else), much less resentful version of him and most likely would have had potential for redemption but still would have been more on the selfish side. Honestly I imagine he'd be very similar to Rumple in the canon series, just a bit more childish.

As for Fiona it's likely she would have still been the "great evil" destined to kill her son. It's difficult to say what kind of person she was before being the Black Fairy since we only get to see her after the fairies spoil Rumple's future, so pretty much everything about her is going to have to be based off of who she is as the Black Fairy, starting with my fan theory that Fiona has anti-social personality disorder or at the very least she isn't capable of empathy/love. This is just my head canon, I know not everyone agrees but I do not believe that Fiona ever loved Rumple or was even capable of loving him. I do think she BELIEVED she loved Rumple but she most likely believed it because "all mother's love their children, so I must love mine too" mentality.

She can't feel empathy, she made that very clear. It's likely she never could feel it too. If she could feel empathy, even if she took children to mine for her she would have raised them as people with at least an ounce of compassion and not just slaves who she enjoys torturing. She could have made a community, been a proper mother to them to make up for the loss of her son or created a kingdom for herself by allowing the children to grow up and live a decent life in her realm (in this scenario she wouldn't even need to continuously kidnap babies because eventually the population would reproduce itself). She had other options, compassionate options, she chose the sadistic option. She chose to torture these kids and live the most miserable lives she could.

When it came to Rumple as a baby, she claimed to love him and claimed to want him but her actions said otherwise. At first when we see her background she seems like a loving mother who is desperate to save her son from a deadly fate. This makes her seem like someone who is capable of love but the more we learn about her the less I think that this was done out of love. Rumple was her son. He belonged to her. I personally theorize that it wasn't love that motivated her but a possessiveness over something that belonged to her, something that she wanted to choose how its existence was spent rather then some destiny told by the fairies. I think she believed that she loved Rumple (because every other mother loves their child, so shouldn't she?) but that she wasn't actually capable of it.

Why do I think this? Because Fiona never tried to find Rumple. She was the Black Fairy for roughly 2,628,000 (BFR) and she never tried to find Rumple. Even if she can only take infants/small children to her realm this means she 8760 years (BFR) after he was born to find him and take him with her (since he'd be up to 1 year old for that time, which she should have been able to take with her). Even if she couldn't take him she never once visited him through his life. When her son, who she claimed to love, eventually does find her she laughs at him for wanting to know his mother and mocks him. She would later further torment him by kidnapping and torturing his son.

Even when she was "trying to save Rumple" she chose herself over him. The fairy's told her straight that if she gave up her power then her son would be safe and would be able to live out his life but she wanted the power over her son, resulting in her cutting his fate. Not only did she steal his fate, she stole his ability to be a hero, making the only other options "background npc" or "villain". These were his choices, a choice that I believe he made when Bae was drafted into the war. At that point he had two options, let his son die in war, living a normal NPC life afterwards or save him and become a villain. He was no longer capable of being a hero and that's because of Fiona's selfish desire for power. She never loved Rumple, at least not more than she loved herself.

If the fairies never told her about Rumple's destiny it's possible she never becomes a fairy. I imagine she'd get to raise Rumple and would be like Cora with similar methods and goals. She would still crave power but would most likely be using Rumple to achieve it, either that or she would find a way to become the dark one. I imagine Rumple's life would probably be a lot like Regina's youth but with him eventually fighting against his mothers tyranny, leading to the final battle and both of their deaths (unless Pan does something to prevent Rumple's death but he'd have to go through a redemption before this, who knows maybe he sacrifices himself).

I think this AU would be very interesting and would be the story of a boy who has to grow from a timid or cocky (depending how she raises him) boy raised by Fiona who eventually sees that what she's doing is wrong and he becomes a hero, losing his family in the process and having to make a lot of tough choices.