Hell, June couldn't take ONE child out of Gilead, her own child, that she obviously knew and could control, while the escape was still somewhat possible. Her second child, again, only one child, nearly died in the attempt to flee the country. Granted, she doesn't know that, but she knows how her previous escape attempts went. Also, she knows that a Martha got executed because she simply agreed to let a biological mother see her daughter. There are astronomical chances that at least one of the Marthas would somehow draw the unwanted attention to herself and it would be enough for the whole plan to fall apart. Or maybe Natalie was the only snitch in Gilead and now that she's gone, all secrets are safe.
And now she thinks that getting 52 random children out will be smooth sailing? Well, maybe it will because they've now apparently opened the Fred and Serena Magical Road to Freedom, so they shouldn't even bother with Billy's plane and just take that route instead