Ok, lets presume that Grandfather's code of ethics was passed along to the Droyne he saves from extinction in the form of the Coyns, knowledge of their use and culture he gave them. What culture they had before his arising can only be speculated, but I do not feel that it was the same as exists in the current Imperium. What they follow for culture in the 3rd Imperial era is entirely artificial.
That being said, it is the norm that when a member of the Droyne species outlives its purpose and usefulness, they commit ritual suicide as not to become a burden to society, or they become one of the "deathless", ignored, shunned and outcast from the entire species. In essence, a death sentence.
I believe this aspect of their culture to have been added after the great-war in response to the actions of his children and grand-children refusing his orders to cease their independent research and return to aid him. (Their research was, according to him, interfering with his own).
This means that by the morals of "today's" Droyne, Grandfathers actions were entirely moral. Judging by the actions of the final war, this may not have been, and probably was not the case in Droyne culture prior to his introducing the Coyns, and the knowledge of how to use them.
If this speculation is true, it also means that Grandfather is not a moral being, but rather a Rational one. One who destroyed the culture of his entire species to ensure that his own parent species never acts against him again.
The real question is why he still remains in hiding. Why should he hide? If he really has destroyed all his children and grandchildren, then their experiments no longer interfere with his own, and there is no one to stop him from ordering Known space to his whim. His hiding and acting in secret hints that either the final war is not yet finished (Mongoose Traveller explores this idea), or there is something (or somethings) else in the galaxy that have the power to resist his will and world destroying, universe altering power, and actively either does so, or will do so if they discover him.
With the new rules for tech levels beyond 15 and the Galaxiad map in T5, I can't wait to see what truly advanced cultures exist in the universe of the 3rd Imperium. What little I have seen revealed about it to date has me more than a little curious.