Why should she lose her kid just because he's human? He's clearly got a magical nature. Any fellow krakoans who'd give her crap over it are garbage people. The story looks like its drawing a parallel between Jube's role as a mother to a human, which is nurturing and loving, and -A-'s role as a father to humans, which was neglectful and abusive.
Remember, Akkaba's leadership is primarily derived from direct descendance of -A-. The purer your blood connection to him, the higher you stood. But even mutants as strong as him could still have throwback children, and he's had a lot of kids over the years. It makes sense that he'd teach these squibs magic so that they'd still be useful to the cause. Which is actually horrible, since he still planned on purging them later. What a horrible dad.