Principle of Double Effect and Moral Indifference

The first of typically four principles in meeting the criteria for the Doctrine of Double Effect is 'The Nature of the Act' condition.  This states that the act itself must be morally good or at least indifferent.   We may cause moral harm in the pursuit of a moral good, IFF our means of doing so are morally good.    This calls into question the intent of the action.   But what of our motives?   Are these such that we know with certainty our intent, or what is morally good in every situation?   What precisely does indifferent mean here?   What kind of attitudes do we adopt that might qualify as 'indifferent'?  In a Kantian sense this means removing our subjective selves from an objective aesthetic experience, yet in terms of moral concerns this seems lacking as it is precisely our moral subjective selves under consideration.  

Aquinas' in Summa Theologica (II-II, Qu. 64, Art.7) introduces the example of killing another person(s) as an unintended consequence as a justifiable means of self-defense.  But we sometimes understand our motives to be 'by whatever means necessary' in regards to protecting loved ones or ourselves.   And because of this deep seated intent or subconscious motive we may act in such a way that distorts what is morally good, or what is a moral harm.   Perhaps this is why Mill states that intent cannot be a factor as what we understand as being morally good may have questionable motives.   

The Doctrine (or principle) of Double Effect relies on the differences between intended and unintended consequences: under this criteria what is morally good in one context may be morally wrong in another. 

Are cases like Aquinas' example epiphenomenal in that new emergent phenomena arise in life or death scenarios - is this what we might understand as moral indifference?