Many philosophers, sci-fi authors and scientists are of the opinion that any inteligent life "out there" may be so utterly alien to us that there is absolutely no possibility of common ground being found... very few serious contributors think the Star Trek universe where the only difference bwtween sentient races is a variety of forehead appliques is likely...
So, while, as humans, we will obviously have a real tendency to bring our inherent, Earth->primate->industrialised human morality and ethics to bear in our encounters with any new race we enciounter, there is no guarantee at all that we will find anything similar coming in the opposite direction...
Imagine human interaction with any species here on Earth to see the problems presented... arthropods are an excelent model to consider as a range of developed species with very little in the way of common ground to relate to, were they inteligent... but we need not even stray outside our own phylum to stretch the philosophical muscles...
consider the mind of a crocodile, shark, or big cat... any primary predator will do... they are utterly without mercy, pity or empathy for their prey... they take only what they need to survive, yet no amount of reason, pleading or bargaining will save you from a tiger who has you picked out as dinner.
Sad to say, any contact with an alien race we may encounter may have similar difficulties.
The aliens may not have a concept for "diplomacy", or even "co-existence".
Michio Kaku pits forward the REALLY disturbing notion that other alien races may be so far in advance of us they don't recognise us as sentient... and feel the same regard to our civilisation as we feel towards an ant colony... and you will note that in human-ant colony relations... it is extremely rare for the ant colony to come out of the interaction better off.
So... in answer to the OP... it is eminently possible that relations with alien inteligence may precipitate an us or them genocidal struggle... and personally, I believe that self defence is the right of EVERY organism... so if the genoci9de were warranted as the only possible way to survive the contact, well, so be it, we have a right to defend ourselves appropriately.
That does not mean that we don't also have a duty to respect our opposition, even mourn them, once we are triumphant. But No, lying down and accepting extermination is not preferable to extinction, even if the flip side is the extinction of another race.
Really interesting question.