The yandere mode is on by default because it shows you the consequences of your actions in the end of act 1.
You can turn it off in preferences or sex her once or twice a week.
If she got damaged then you're screwed, it can't be reverted.
Most likely you won't be able to revert it either.
As for Chloe, also no but if I understand correctly the issue of finding out if you can (or even want) to fix Chloe is going to be addressed somewhere during the third act.
You can only have kids with main girls (they have a heart card entry) that have reach love level 4 (not all of them though)
The girls that can get pregnant are: Kana, Pixie, Lily, Jessica, Madison, Veronica, Annie, Asteria, Luna and Emma.
The others haven't reached the proper love level, have said why they can't get pregnant or are a special case (like Gwen and Chloe)
Well, aside from Jessica's friends you can get 3 more characters to move in.
Two you get from the main story, fey lead. At some point you get the choice to rescue them.
Likewise, in Roxy's story you also meet a character that needs rescuing.
Just keep playing, The choice is quite obvious once you see it.