Sorry for not making much post to this topic after starting this thread, because this topic doesn't seem to generate much response although I consider it to be of much importance to everyone. I thank everyone who have read this thread and offered their own comments on this topic.
Personally, I do not believe that the Triple Gem including our Dharma Protector will protect us from our Karmic debtors in the same way as a detail of bodyguards will protect a politician from assassins or like a bomb shelter. If sentient beings can be protected from the collective vengeance of their Karmic debtors simply by seeking the refuge of the Triple Gem, including our Yidam & Dorje Shugden, then sentient beings will be free to harm others to satisfy their own selfish ambitions without fear of vengeance. It's a very simple logic, if you stole something from someone, destroyed their property or killed their love one, they have the right to demand compensation and justice.
Instead the Buddha Dharma educates us on the Law of Cause-&-Effect, Karma. When you hurt others, they will hurt you back. We have to accept the fact that all forms of unhappiness which we have experienced in our lives is the result of having done the same to others in the past., and we definitely have to pay for what we have done, one way or the other. When our karmic debtors comes to us in this life to make their claims (by creating problems and harm) on us, in the form of disagreeable people, spirits or demons, we feel that we are the 'victims' and they are the 'bad guys', we should be protected and they should be punished. We feel this way because we have no memory of the all the wrongs which we have done in our previous lifetimes. If we can remember, we will definitely feel that his or her actions against us is justifiable.
I believe the intention of the Triple Gem is to inspire us to understand this and accept the fact that we have to pay for what we have done, and inspire us to take the appropriate actions to make up for all our past wrongs.
Yidams and Dharma protectors like Dorje Shugden will not destroy our Karmic Debtors. Why? Since they are emanations of Buddhas and Bodhisattvas, they definitely possess Bodhichitta which means they cherish all sentient beings like their only child. Since that's the case, we can't request them to attack someone just because they have been causing problems for us, in fact it is against the Dharma to make request to Yidam or Dharma Protectors to attack anyone. If the person is indeed harmed after making such a request, I am sure it's not your Yidam who responded to your request. Simple logic, your friend owe you some money, when you ask him to repay his loan, he denies this and attacks you, would you be pissed?
The correct way to put an end to the feud between all our Karmic debtors and ourselves is to make requests to our Guru, Yidam and Dharma Protector to inspire us to take the appropriate actions to pay off our debts to each and every individual karmic debtor from all our previous lifetimes, as much as possible now especially since we practicing the Buddha Dharma in this life.
We should dedicate the merits from our Dharma practice to our Karmic debtors as much as possible. By the merit of such dedications, may they regain the happiness which we had robbed them of in all our past existences. We can't take back what we have done, but we can now try to return back the happiness which we have taken from them as much as possible, out of sincere remorse.
One point of interest, In Southeast Asian countries, it is known that Buddhist have pujas and dedicate the merits to their Karmic debtors during the Ullambana Festival, which doesn't seem to be celebrated here in the West although this festival is based on the Ullambana Sutra.