Ruin her life?
I can think fo 1001 ways a kid can have their life ruined outside of their
first name.
(Death, abuse, learning difficulties, sickness, poverty)
You know... more concrete reasons that usually our outta our control.
As mentioned before, if a parents raises a child right, no matter their name (to most degree), they'll be proud of it. Nagisa can be said in English without much blinking from others as to 'it's an anime character!' And if the kid isn't into anime much, all the better then.
Once the OP becomes a mother, she may not have time for anime or will find that watching Disney with her kid would be more fun.
As Vexx pointed out, there are actual Japanese peeps with this name, the first thing you get on google is a resturant.
And the kid won't be conscious of their name until at least 7 years and older.
So who the hell knows what'll happen in 7 years or how Americans will take to the name or what changes will occur in schools. It's the country of where celebrities are naming their kids Apple, Rocket or Audio Science or Kal-El.
I'd be relieved tbh, lol
As for bullying, most kids aren't into anime, this is an anime forum (which again OP, seriously go ask regular people on the street and in town to read the name and see what peeps think).
I know from our point of view the reason seems superficial cause we know the source (an anime) Thoghu had the OP not have said that, I'd have known no different, expect that it's Japanese origin and that's it.
But if the OP explains the source as somthing different or simply
'I like this name and it's special to me and you're my special little girl'
The kid won't think much of it.
As for bullying?
Kids will bully for anything, hair, height, teeth, clothes, speech, words.
How one handles themselves is what it comes down to and the area one grows up in.
So yeah, ruining their life, not quite...