spoilers:end of spoilers
Plenty of evil people manage to retain being loved by their children. Familial bonds can be complicated. As far as we know her cloned mom is still kicking around somewhere, presumably in jail. That might be what she wants for the others, it certainly appears to be possible.
Of course, knowing that Alex is the only other team member to still respect their parents Molly might just be lying to him about bringing them back. She might have her own agenda for wanting to travel with Alex, and just used bringing their parents back as an excuse to have him let her tag along.