The desired ending for Myst is when Atrus destroys the linking books to his sons (he doesn't kill them, but they are forever trapped) and he gives you full access to the library. And then Atrus just sits there, ignoring you while he continues to write in his books. He does mention that he is fighting a greater foe. This foe will be in the sequel to Myst. And yes, this foe is a greater danger than the two brothers would have ever been!
There are four different endings to Myst. Have you found them all?
Go back to Myst Island -- The end...decision