I would disagree. I re-read your post a number of times before replying. You state that the doctor found out something about his own father during a medical consultation which implies he was treating a family member which is against GMC guidance hence my first point.
To clarify the other point (and my main reason for disagreeing), if an applicant deliberately fails to mention a feature of his medical history, of which he is aware (whether personal or family) then he is on very stick ground indeed. To use an example...
Huntingdon's Chorea is an inherited condition which often presents in late middle age and frequently after the 'victim' has had children. It leads to progressive deterioration in neurological function. I would be astounded if the CAA took anything other than an extremely dim view of any person who applies for a pilot's licence and fails to mention this inherited condition as its implications for that pilot's fitness to fly are immense.
I will concede, however, that a second cousin twice removed who once had angina does not in and of itself constitute a family history of ischaemic heart disease.
It's a matter of degrees. If the family history may impact on your ability to perform your duties as a pilot then it is relevant to the application and the CAA medical department have right to know. It's a matter of public safety where the needs of the public outweigh the individual's right to confidentiality
bob