sukkalApril 26, 2012@40mercury,
You are so right that “the human element is where its gets compounded and complicated.”
But, we tend to elevate ourselves ABOVE the rest of nature on earth (and in certain religious belief systems, even beyond earth). In some ways the premise of the Engineers possible role in this film supports this idea that we are “different” (by having been artificially manipulated by them). But, the philosophical debate can always be escalated to a higher level. Ultimately, the Egnineers (as products of evolution within the known universe) are also ‘natural’ (as far as we know). So it may simply be their nature to experiment on/with us. And, as I've mentioned elsewhere, their civilization may have "run its course" and the last fragments of what they oncewere may be engaged in "desperate acts for survival." Even we humans have social (and moral/ethical/emotional) mechanisms in place for comprehending and forgiving acts of "evil" (= intentional harm) when they are tied to self-preservation and survival.
It's also interesting to note that not all human cultures (and corresponding languages) have a word for "evil" that carries the same meaning as it does in Western thought.