My own take on the Elder Ones is that they are not inheritantly evil. In fact, they have no morality at all as we would understand it.
They simply want things to be as they want them to be, and we are so far beneath their consideration that when we are destroyed/maddened/etc by them, it is of no more consequence than the bugs that die on our windshields each day.
We, being the bugs, intepret this as evil.
So, at least to me, the trick would be to have "how they want things to be" to somehow be inline with a positive outcome for us bugs, which we would thereby (incorrectly) ascribe to them being good.
Make sense?