Again, not a lawyer, but from what little I have understood, the President is bound to go with the advice of the new PM in case of a new Governor, but an existing Governor serves at the pleasure of the President. Would be happy to be proven wrong though.
As for the rest of your comment, completely agree. You cannot have selective ethics in this whole fiasco. You cannot have CM elections from the gallery, you cannot have 25 people disqualified but still be in government, you cannot have so many things.
Democracy in this country is a sham.