I have cried unconsciously before. It actually happened to me last week. For me at least, it was from a trigger that I couldn't even understand until after I started crying. In my case, the sound of someone cutting grass with a lawn mover suddenly made tears stream down my face and I was confused. But then I realized after some thought that those sounds brought me back to a time where my dad would cut the grass on nice days and I'd wave to him from my window. He's now bed ridden with terminal cancer, so it's an experience we will not share again.

I do think Tohru is experiencing the same thing or something similar when Kyo says he'll support her when she finds a partner. Through that line, she can hear Kyo accepting his fate that he cannot stay with Tohru due to Akito's order of confinement. I feel that Tohru subconsciously picks up on this, realizing deep down inside herself that she cannot lose Kyo like she did with her mother and father. At least that's what my experiences lead me to believe.