Tadashii Kodomo no Tsukurikata!

he can't marry her and must make babies with her, sure he can do that but what if he also makes other babies with other girls? And what about that naked chick?

On a serious note, sometimes there are genetic dependent disorder that remains dormant such as thalassemia but only active if his/her partner also got the same dormant genes.
Let say half of his gene carried the disease, if he married a normal partner the disease will remain dormant but his offspring still carried 1/4 of it. If his partner also have the disease, then his child will have 1/2 of chances to inherent the disease and 1/4 of probability to get active disease in his/her gene. That why some government encourage people to take test before marriage to prevent these type of disease inherited by their child.
The marriage is not the main focus I think, its the act AFTER it that is related to his transfer of gene (please tell me you understand what I mean:D)

Hmm, maybe another plot arc may be that someone else goes back in time and does want to kill him.

And my guess is that the guy doesn't want to kill Yuu because that they're somehow related. Granted, changing the future would probably change or entirely remove the future person's existence, but maybe he wants Yuu to still live a happy life? I don't know. It's just one chapter so far and so this is just pure speculation...