This sounds like it could be "Ambassador" by Peter Watts, which can be read on his website for free here.
It hits many of your points, starting with a pilot making first contact and getting hostility:
It always found me. I still don't know how; theoretically it's impossible to track anything through a singularity. But somehow space always opened its mouth and the monster dropped down on me, hungry and mysterious. It mighth ave been easier to deal with if I'd known why.
What did I do, you ask. What did I do to get it so angry? Why,I tried to say hello.
What kind of intelligence could take offence at that?
Eventually destroyed by bigger fish:
We came through together.
Cat and mouse dropped into reality four hundred meters apart, coasting at about one-thousandth c. The momentum vectors didn't quite match; within ten seconds Kali wasover a hundred kilometres away.
Then you destroyed her.
It took some time to figure that out.
All I saw was the flash, so bright it nearly overwhelmed the filters; then the cooling shell of hydrogen that crested over me and dissipated into a beautiful, empty sky.
I couldn't believe that I was free.
Musings about intelligent spacefaring life needing to be aggressive:
I've stopped trying to reconcile the wisdom of Earthbound experts with the reality I have encountered. The old paradigms are useless. I propose a new one: technology implies belligerence.
Talking about how techology rises until a race is comfortable and stops being aggressive towards its own environment:
All rested, eventually. Their technology climbed to some complacent asymptote, and stopped—and so they do not stand before you now. Now even my creators grow fat and slow. Their environment mastered, their enemies broken, they can afford more pacifist luxuries. Their machines softened the universe for them, their own contentment robs them of incentive. They forget that hostility and technology climb the cultural ladder together, theyforget that it's not enough to be smart.
You also have to be mean.
And even your memory of the pilot being genetically modified and missing some key ingredients of humanity tracks:
My creators left me a tool for this sort of situation: fear, they called it.
They didn't leave much else. None of the parasitic nucleotides that gather like dust whenever blind stupid evolution has its way, for example. None of the genes that build genitals; what would have been the point? They left me a sex drive, but they tweaked it; the things that get me off are more tightly linked to mission profiles than to anything so vulgar as procreation. I retain a smattering of chemical sexuality, mostly androgens so I won't easily take no for an answer.
There are genetic sequences, long and intricately folded, which code for loneliness. Thigmotactic hardwiring, tactile pleasure, pheromonal receptors that draw the individual into social groups. All gone from me.