I was thinking that was really odd but after I thought about it a little more it is probably a counter measure against inbreeding. Still seems like they shouldn't need to send them away when they are think little but I guess to make room for the next litter? Cute story though.
From what I gathered, due to the low population rate, he decided to give away the litter of 6 to other families. I guess there are many couples that are unable to have children and since he is a rare male Omega, guess he is helping with the population issue. You can see in that last part when Kin tells Ise that they are keeping Tou and will raise him as their own, but the others will go out to other families in need. I guess it has to do with the ratio of Omegas to Betas to Alphas. Also, like the other person states it could also be a way to prevent inbreeding. It was sad to see him give then up, but it seems like it's almost a rule or law...how it seemed to me....and he planned to have more children....so reminds me of a breeding program when a species is dying out....and they did mention the dwindling population so who knows? ┑(￣Д ￣)┍
It was good until the ending. The ending actually sucks. Given up their babies really?? (╯°Д °)╯╧╧