Many eps and situations happened without a word or acknowledgement of the kids and civilians on the ship. You'd think it'd be a major factor in all those conference room meetings.
That's where my idea of having two ships could've helped -- if they needed to do an episode like that where the ship was on a mission that was inappropriate for the ship with all the civilian scientists and families aboard, then it could've just focused on the military escort ship and left the big research ship behind. Kinda like DS9 episodes that focused on the Defiant
rather than the station -- except that DS9 had the same people in charge of both station and ship, which never really made sense.