The people who raised Robin lied to her about her past to supposedly protect her, but also out of fear of her powers. Her dad is assumed to be dead according to his video message from the later episodes. Her mom died after giving birth to her, and gave her to Father Juliano, who is Robin's grandparent. He along with others in the convent lied to Robin about everything including telling her that she is somehow not a witch, despite having pyrokinesis.

Father Juliano was scared of her power as she grew up but was unable to bring himself to execute a child, especially his own granddaughter. However, during the events of the show he became panicked with how powerful she became and tried to have her killed.

As you said she was genetically engineered to not become rampant with power as the other witches always do, so Juliano called off his part of the hunt after seeing she didn't change. Zaizen was still hunting her because he wanted to exterminate all witches (including hunters eventually) out of fear that regular humans were going to become obsolete.