When you are young, these things can seem huge. You lack perspective. As you get older, you will start to wonder why you made so much out of this.
I don’t know how you can be expected to understand that someone is saying they like you if they ask if your Dad is nice. That is just way too obscure. It’s just a question. It’s not flirting. It’s not an invitation to date. So I think you are misinterpreting it.
I don’t see how you rejected him. Maybe you were rude. But who among us haven’t been rude on occasion? You should forgive yourself. You didn’t reject him.
Also, he had a girlfriend. So it would have been inappropriate to encourage him. And now he is in a different city, so it would have been bad if you had tried to get together with him. Now it would be worse, because you’d miss him horribly.
So you did just fine, and have nothing to beat yourself up about.