Because she's realised there may be more than one way to survive
Lisa Joy (co-creator/showrunner) explained at the Hollywood Reporter
She's changed her mind. She's changed her philosophy. She realizes she has but one path to potentially securing the hosts' safety, when she helps see through Maeve and Akecheta's plan by securing the sovereignty and safety of the Sublime, to which many of the hosts have escaped.
It's an acknowledgment that there are paths other than hers that she needs to be tolerant and accepting of and can't stand in the way of. It's much like how she tells Bernard that she understands they will likely be at odds. They will likely come into conflict. They may even kill each other.
But she's come to understand that true freedom isn't something that arises from a lack of dissent, from a dictatorial or totalitarian rule of one set of ideologies. It's something that has to happen with a plurality of ideas, sometimes coming into conflict.
Because she's learned her lesson, she's bringing Bernard back into this world to be a check on her own power, in some ways