[He's not surprised. It hurts to hear it, but it's not surprising at all - Kitty's tough as nails and he's having a tough time even imagining her crying.
By now he's really run out of words, and so he settles for a noise. It carries a big message for being just a noise: sympathy, empathy, a deep desire to make things better. A dislike for how often the good of the mission goes ahead of the good of the people on the mission. Even an undertone of wanting to have had this conversation in person, if only so he could've given her a hug she probably would decline.