Not gonna lie...this is ridiculously wholesome and wish it'd stay like this.
But if he is the ML, I don't mind too much as they're not blood-related and I don't view it strictly as incest...but it really straddles the line as they are growing up as siblings. Though, if the MC knows she is not his sister...and the ML is also aware...it's very eh. I'll be actually more disturbed if and when she develops any feelings for him prior to like 20 years old...she is technically an older individual who probably should view him as a little bro. Though, considering some of her actions, her baby emotions/feelings are pretty strong (otherwise she wouldn't get as easily as upset?).
In fact, I'd find it more hilarious and prefer it if she strictly views him as a lil bro while he becomes a ridiculously overprotective big brother that she humors. Shenanigans abound! Though, the setup to this fic is pretty dark soooo...yeah.