Where to start with this one? Lots of fodder for discussion.
On first listen I thought it was pretty good. Not spectacular, but pretty good. The fact that he was a suicide soldier sent to kill the civilians was very clear early on, though it seemed to be intended to be a surprise. Most noticeably when he said something like "I'm here to save you from the aliens," I said truthfully. Any time "said truthfully" is used, I immediately analyze how that phrase could be both truthful and misleading and in this case I came to the immediate conclusion: he's gonna kill them all. I guess many of my reading habits were formed by reading the Wheel of Time series, and reading about Aes Sedai really makes you watch meanings very closely in cases like this.
One of the most interesting things about first contact that I always like hearing about is the establishment of communication and common language. For anyone else interested in this topic, I strongly suggest you check out the works of Juliette Wade. She's been published twice in Analog, both first contact stories based around establishing culture/lingual relationship with alien species, both very good. And she has a great blog, one of the few that I bother checking back on:
http://www.talktoyouniverse.blogspot.com where she often talks about language's usage in SF and fantasy, among many other interesting things.
Anyway, the reason I brought up the language thing is that it's not clear that the Shardies are CAPABLE of communicating with us. The humans blame the Shardies for not responding to communciations, but they seem to assume that the Shardies are capable of both receiving and understanding radio (or whatever technological) means of transmittal. Even if they can see a signal, and can see pattern in the signal, they're not going to know how to interpet it in a meaningful way. Even if we saw them face to face and tried to talk to them, there's no saying if they have auditory sensors or some other means of communications. Perhaps they are telepathic and because we don't respond to them with thought messages then they assume we are unintelligent. Or maybe their sensory organs respond only to electromagnetic waves, and by blasting them with hailing calls we actually managed to overwhelm and blind and/or kill one (like an alien race that communicates through lasers and accidentally flash-fries a human on first contact when he tries to say "hi"). I mean, we don't even know what their physiology is--the ships themselves could be the race! Assuming that all the information given in the story is verifiably true, I'd say it's safe to say that the aliens are intelligent--they are capable of building starships, of tracking trajectories of other starships, and can extract living brain from an organism and wire it to their existing technology. But it's not clear to me, even if everything in the story is a fact, that they are necessarily any more aggressive then we are. Perhaps they think that WE struck the first blow and after that they were only reacting.
It seems like the main point of the story was to show that it in an extreme circumstance it could be considered justifiable to kill in an act of mercy. But I've seen this theme elsewhere, so that wasn't all that inspiring to me. Back to the Wheel of time, early on in the series there's a situation where a man and a woman are traveling together, and they're threatened by something which if it reaches it is abundantly clear that it will kill them in an excruciatingly painful way. He plans, at the last possible moment, to kill her to spare her the pain--luckily he doesn't end up having to. I was horrified by it at first, but it makes logical sense. I don't think that I would have the strength to kill in that situation, but for my weakness another human being would suffer terribly and would still die.
BUT what made the story even more interesting for me was the mention in the comments about the possibility of propoganda. Then things get REALLY interesting. The entire story is through the point of view of the soldier, who only knows his knowledge from what the government has told him. We all know that governments never lie, right? Especially since we don't know anything about the government, I don't think we can rule out the possibility of propoganda. Maybe the humans intentionally attacked the first Shardies. Maybe the Shardies don't actually use human brains, that was just an attempt to dehumanize the enemy to suppress teh possibility of public outcry at killing another sentient race. Maybe there are no Shardies at all, maybe the intergalactic federation of planets was in a state of civil war, and someone decided to create some AI ships and put some brains in there to create the illusion of a common enemy in order to unite everyone against them.
It's very possible that I am just channeling the mindset from one of my favorite games of all time--Deus Ex. Fan-fricking-tastic game with nanotech, dozens of conspiracy theories all tied together into an intricate FPS plot.