I'd probably say something like...
"Okay, so you guys want to destroy humanity because we're worthless, but how would you define worth, some magical commodity that is required for just existence?. And you call yourselves logical?. the truth is that when you say worth you mean useful to a larger quantity of lifeforms, but why does that set of lifeforms matter?, why does life, the universe, ANYTHING matter?. The idea of an inherent value in the mass entropy of the galaxy is a simple coping mechanism we invented because somewhere along the line we decided that everything had to have a reason, that everything had to operate in service to something bigger. But does a wolf ponder the meaning to it's hunger?, does a star calculate the meaning of life as it erupts into all consuming inferno?. In the end, nothing has inherent logical meaning, because the two are naturally separate from one and other. Meaning is a commodity built from emotion and impulse, these things are wired into our brains because without them we'd be doomed to apathy. Meaning is what we use to differentiate when we have to make a choice, using logic to uncover deeper, less obvious emotions, to understand not only what we feel, what we felt, what we will feel. If you destroy us do so in the knowledge that you don't do so for the greater good, you do so because your so insecure with yourselves you have to justify yourselves by hanging on to the illogical belief that your somehow above us, you need less powerful lifeforms to feed your ego. You want to be logical?, accept the fact that nothing you'll ever do will make you inherently better then anything else, because according to your precious logic, we're all just the same mutated organic matter"
of course this is assuming that the aliens are destroying us out of some misplaced sense self righteousness. I figure, best case scenario, they commit suicide in redemption for their ignorance and we get to scavenge their technology. Worst case scenario, they decide what I said doesn't make jack shit sense and they kill us all