Then I do not understand what is the purpose of this organization in the first place. They organized this big gig on the ship to rescue people/stop human trafficking and they only found one girl right? They expected more yet they called it a win. MC on the other hand saved kidnapped kiddo and this mean shit to them? To doctor too? Because basically that is what MC has done, saved him which would not be possible if he just ran away. They were not there so without details all they know he got back with a kiddo and got serious fight, especially doctor couldn't know if he could run away at the right moment (as far as I remember he only told it to Fiona) so she is just being hostile to MC because she likes bitching... Another reason to turn away from them
Your understanding is correct from player perspective, as you experienced it all and thinking about it she may be right, he could just run away (especially that he was not aware of kidnapped kiddo is there) but yeah, she is not player here and knows shit about what happen.
In perfect scenario they didn't expect combat yet things are not always perfect and if combat was not an option, they would not be thinking if sending him there is either good or bad idea, they knew combat may happen.