To say that she was surprised by his instant defensive stance would be an understatement. Isabella managed to suppress her surprise and stand steady until Raphael was able to come down from the intense instinct to fight whatever might be coming for him. She realized that this must be linked to his abilities, something like when she threw a piece of candy and he snatched it from the air before it could hit him on the couch. His emotions were exposed, making him more susceptible to the instinct to fight back. To be honest, she was probably damn lucky he hadn't taken a swing. It might have ended very badly for her.
When Raph drifted past her, Isi stepped back inside and closed the door softly. She felt it best to just give him a minute, but it would also give her time for her heartbeat to slow. She wasn't afraid of Raphael, but she wasn't completely immune to the fight or flight instinct. Flight had really been on her mind for a brief moment.
Rather than jump into questioning the young man, the good doctor took slow steps to the chair behind her desk and seated herself. She felt it best to be patient and wait on when Raph would like to talk about what was going on rather than pressuring him into speaking. He liked to be in control and so she was going to allow that. At least until he gathered himself together.