I almost forgot that Ruby didn't even know that the doctor was Aqua.
She died without knowing that the doctor also passed away, right? She might still be thinking under the assumption that he's still alive...
That being said, based on the raws and my extremely limited understanding of Japanese, the way she talked about him sounded more like a respect/familial love as acquaintances more than anything else. I doubt there's anything more than that to go into.
Also Kana is best girl. Still calling it.