Why would he not get her out of the pool? The best way to protect her secret would have been to act as if she was a real girl, get her out of the water, send her Bakayashiki to look for help, and hope a replacement came along while no one was watching. They could then say she was drowning but recovered after CPR or whatever. Instead he avoided going into the water and went along with the dumb idea that she was an alien. Was he planning to just stand around with her indefinitely, making it obvious that something weird is going on?