Alexis was a sensitive girl that got teary when she heard about dolphins getting caught in nets or saw roadkill. She wasn't even feeling guilty about what she'd said anymore, she was just genuinely upset about what had happened. River's explanation had Alexis almost crying.
Alexis tried to get herself under control. She didn't want Simon feeling like he had to comfort her too when he had his hands full with River. Since River seemed to be calming down, Alexis shouldn't be getting so worked up. They were okay now. They would be safe. She couldn't speak without her voice cracking (and what would she say, if she could?) so she just nodded to Simon.