If the alien value systems weren't comprehensible how could we explain it in a story? Even if we didn't comprehend it, we could probably still figure out if they deceive. If they don't, we just figure out their demands and decide if their acceptable. If the demands aren't, we either try to wipe them out or flee. If they do deceive, we can either guess what their final plan is, or wipe them out or flee. We wouldn't fully understand their values and we don't fully understand other humans values. When I see moral dilemma I realize I don't fully understand my own values. The only way to understand another beings values would be to share thoughts and since we could never know if the thoughts were being shared accurately, we couldn't be sure what others really value.
It was said that the aliens would not accept gamete reproduction because they ate children before they knew what evolution was. They did it because it increased the number of surviving children from each pen/ couple. If they are still culling to increase the success rate, than a new method that increased their success rate would be preferable. In the story, gametes are better for evolution than culling so gametes would produce more surviving off-spring and would thus be preferable to culling.
I said "in the story" gametes are better because I disagree with the author on which is better for evolution. Producing good gametes will allow one to get an off-spring instead of rival mates, but the best gamete doesn't necessarily make the best off-spring. Gametes are selected by which one is the best swimmer and which has the best 'sense of smell'. It could be coded to produce a child with extremely low intelligence or extremely poor muscle tone, or unable to get glycogen out of their cells (Pompe). If out of the millions of sperm emitted with each ejaculation, the best tended to win, there would be much lower rates of genetic disease.
They said that the alien would expect that if Hitler were bad he wouldn't have been made a leader or would have been killed. Most of the world disliked genocide, but the Nazi, being loyal, liked what ever Germany was doing so they liked genocide. This group was wrong and is the reason Hitler was the leader. I'm not saying the author messed up due to this ; its just something I noticed. A potential flaw was it was said if Hitler had been bad humans would have killed him. We did try to kill him and then tried the people who protected him for war crimes, although the Nazis being a group, it might have been seen as a 'reasonable error" esp. since most Nazis weren't killed.
This isn't the prisoners dilemma since the there are three options: continue with deflectors down, put defectors up, or attack. More importantly, putting up one's defectors does not hurt the opponent like it would in the prisoners dilemma. Also, the humans putting their deflectors has the same effect on their safety as attacking since they can destroy the other ship or block their attacks.
More importantly, about the aliens, just because a large group made the mistake doesn't mean it was reasonable. Look at the Nazis, the Russian Communist under Stalin, the Romans and their killings, the Aztecs, and the Salem Witch trials. There are plenty of times when large groups do things that could easily be figured out to be wrong. Cultist and prostitutes working for pimps are some strong examples IMO. Instead of allowing others to live because they were part of a group their ideas should be considered and if their logic was sound enough, they should be allowed to live.