Maybe he hated kids?
If they did become the Futruans then any number of reasons could have resulted in a LA/ Military reigeme, perphaps it didn't even become one until after his death years later and the offspring of these people raised in a harsher and more military culture that in turn when exploring the galaxy became seperated and became even more militant.
Another explanation that occoured to me could be that they wern't even part of the Futurans, it's safe to assume that gate Travel to other planets would have happened a fair bit especially in the early days. Once the LA members had fully been accepted into the crew they could have been sent on a mission along with military personal and a few civilians this mission could have been seperated and unable to return. Embittered by this, Eli's failed decision to try and get them home and their predicament they grow to hate the other members of the destinys crew for not coming to their rescue. This hatred filters down through the generations which with the LA and military influence becomes a militant culture with none of the values of the destinies crew. Perphaps the discovery of a seed ship or war with aliens or drones would have led to great technological expansion and the discovery of FTL. Due to war with the drones they are forced to leave this galaxy and settle in the next one where our crew meets them.