In respect to ensuring that the royal line is kept as good stock its usually helps to have a good assasin around at all times to make sure that the heir to the throne will be a strong king. While I appreciate the fact that killing your own son just to ensure the success of your progeny is a bit harsh, a nation needs a strong king. In MTW an army commanded by the King recieves a morale bonus (so long as the King doesn't rout or die in which case the morale penalty is much higher). If the King is a 7* plus general, this can lead to unstoppable armies.

I would try to ensure however, before killing your heir, that you will still be left with at least an heir and spare. And make sure the assassin is competent - otherwise you could get a civil war or at the least very plummetted loyalties from all generals.