The separation of genders come from experiences, that were made in centuries and countries, that had no separation o genders in prison.
If people of genders meet each other, there will be sexual realtionships, leading to the possibility of children being born. The solutions of the past for those kids were either to be kept in prison for them, which caused them to have a highly chance to become criminals as well, simply because of the "bad surrounding" or they were given to orphanages, just as it is still custom in our countries, if both parents are on accidents both in jail. But while you cant influence free people to go in jail or not, or to have children or not, you can at least care for kids with both parents in prison, being conceived on purpose.
I have no prob with the possibility of married partners being able to meet each other, as long as at least one of them is in freedom. As well that I have no problem with special jails existing in my country, for people that are actually responsible for an already existing child, below the age of three. (The inhabitants are not treated special, but there are simply possibilities given to care for a child, as well as there is a playground and a playroom for the kids.) But if both are in prison, then simply none of both has the possibility to care for an created child in an good way, so I dont see the reason, why we should let that happen on purpose.
If people want to have children, then at least one of them not being criminal, is not that hard of an rule I think.