You're right imo. I don't think Karkat was like... Annoyed with Nepeta, even, for having a crush on him, it seemed more like he genuinely felt bad that he couldn't reciprocate those kind of quadranty feelings. It's been correctly pointed out in this thread that Karkat cares about ALL of his friends, but I think it's more than just 'default friendship', because again, he's still thinking about her years later, and from the Roxy dream bubble flash we know that his dead doomed god tier self is apparently palling around with her a lot in the dream bubbles. It was just a friendship that never got to be fully realized.