That's an interesting question.
I'd say that's something anyone that creates characters might struggle with depending on their nature.
While I haven't published anything original that I wrote (fanfiction doesn't count obviously), I did RP a lot. I spent hours writing paragraphs of text setting up characters, settings, worlds and more. I got into their heads, thinking about how they think, what motivates them, what they like and love, what they hate and fear.
...
And then I still subjected them to utterly horrible things for my own entertainment, the entertainment of my partner(s) and whoever else ended up reading what ended up being written.
The reason I did that is because to me, at the end of the day, they're still characters, and no matter how much I may joke about "if they were real, these people would probably torture me to death, slowly, for what came out of my mind".... I never forget that they are not, in fact, real. That they can't suffer, because they don't exist beyond my mind and the minds of the people that read whatever it is that I wrote.
Even when they go off the rails in my writing in some way or another to the point where they surprise me, they're still my characters, and unlike real people, they do indeed exist only for my benefit and the benefit of whoever I choose to share them with.
At the same time, I'm someone who's asocial. Who treats empathy and sympathy as entirely different thing. I can walk a mile in another's shoes, and I'll be a mile away and have their shoes.
Based on what you're saying, I guess you're someone who deeply sympathizes with anything and anyone you empathize with. That's not a bad thing. Maybe it's even a good thing if it's not taken to extremes... But I still think that you should never forget. No matter how cute she is or how real she may become in your head... She's not actually real, neither is her suffering. What matters is the satisfaction and pleasure she'll bring into the real world through the story you'll put her through.
Don't think about her, think about all the people that will enjoy the end result of your work.