I've had the same problem when playing as France or when operating in traditional French territory.(Maybe the designers don't like the French ).
Curiously I have not had a Family member executed whilst they have been in a settlement or castle, only outside. Anyone else found the same?.
When an iquisitor has come sniffing around I have just put my generals in cities and they have left them alone. You do have to be careful to get the generals out of range of the inquisitors quickly when you leave the settlement tho, as I have had a few generals holed up in cities to avoid inquisitors for a few turns, then when I have sent the generals out to attack rebels etc the inquisitors went straight for them and bang one less general.