Its likely a significantly advanced race isn't going to be kind to us.
Do you feel despair when you step on ants on the sidewalk?
Do you feel despair when you step on ants on the sidewalk?
Well no, but neither do I go out of my way to step on them. And I don't see that we'll be so very, very far behind these beings that they're not even capable of recognising we're sentient. Indeed, with all their technology, they should be even more aware of the potential sentience of life than we are.
In the last 100 years or so, humanity has made great strides towards its treatment of lesser animals - we have a long way to go, but it wouldn't be unreasonable to set a goal of zero intentional animal cruelty by 2100. I'd expect technologically advanced aliens to be similarly advanced ethically, or if they do wipe us out, it would at least be deliberate (eg 'the killing star' logic).
Personally, I find that argument a little naive and anthropocentric. Who's to say they need our resources? Couldn't they find resources aplenty in asteroids, on planets closer to their home, or through artificial synthesis? It makes little economic or biological sense to go through the trouble of exploring vast, deep regions of space purely for the purposes of acquiring resources. (And that's even assuming they need the same resources we do, in the first place.)
In all likelihood, an alien intelligence that made itself deliberately known to us would be doing it for scientific or diplomatic reasons. If they want our planet, they could just take it. There'd be no need even to deal with us; they could just lob a few asteroid-sized objects at our planet, eradicate life on the surface, then come in and harvest away.
To your point: any sufficiently advanced intelligence that's going to bother interacting with us will probably have studied us well in advance. It will know as much as it can about us. It might (depending on its alien mindset) have a good understanding of our potential sentience, and a respect for sentience in general.
The real threat isn't from alien intelligence, but from alien AI. A dumb AI, at that, of the kind that mindlessly travels the galaxy, self-replicates, and harvests material without discrimination. But again: a race advanced enough to develop such technology would probably be aware of the consequences of letting it run amok. There would be checks against that scenario by design.
We're very quick to ascribe a bleak, law-of-the-jungle amorality to alien intelligence. But let's think about it. Such an intelligence had many "tests" to pass: a nuclear age (or some equivalent thereof), climate change (or some equivalent thereof), wars, and so forth. If it's far more advanced than we are, it probably passed and survived all those tests to get there. It's very hard to pass those tests in the absence of a complex, well-developed ethical system.
Frankly, I don't think it would end well at all (even if they are benign). We are too smart/proud to let someone set the rules for us, not after being at the top of the food chain for so long.
What we want to avoid is actually the much more destructive force of the 'modern civilization' of organized corporations, like the East India Company.
Don't have too much confidence in that. If a civilization creates AI, it could possibly improve itself and become incredibly intelligent, but still keep the simple goals that it was originally programmed with. Thus endlessly self-replicating, consuming the universe to create bigger computers, or destroy threats to itself, or preserve it's existence as long as possible.
That probably doesn't matter very much to the ant.
Those ants are pests, I pour boiling water down their holes and leave poison around my house because once in a while a few get on my counter, or they cover the sidewalk when they go to war with each other. I have a pet rabbit, vermin, but I put out mouse traps.
An alien species entire reason for making us extinct or pushing us back to the dark ages might be as petty as because we were a visual nuisance, or like Douglas Adams suggested: we got in the way of road construction.
There is no such thing as "advanced ethics". Our human sense of morality evolved under our specific evolutionary conditions. Aliens would be completely different. Even worse, they could be taken over by Paperclip Maximizers (http://wiki.lesswrong.com/wiki/Paperclip_maximizer).
An interesting short story about aliens that are very different from us http://lesswrong.com/lw/y4/three_worlds_collide_08/