Affair?
I wholeheartedly admit that Martin's character was creepy, but where was the actual affair? What could she possibly have written (other than her personal feelings for him) in her diary that would be considered incriminating to him?
As far as I could tell, she didn't know he was giving her the wrong medication and she was asleep and unaware that he creepily kissed her. He didn't seem overly flirtatious with her and the "relationship" didn't overstep doctor-patient boundaries to her knowledge.
So, what was Martin so afraid that the diary had written in it and then subsequently warranted the flushing of the pages down the toilet? He killed a man for that book and yet, the movie failed to share this vital information.
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"...To thine own self be true..."
William Shakespeare
Hamlet