If we are going to stick to conventions, captured aliens should be treated respect for their persons and their honour and may not be subjected to physical mutilation or to medical or scientific experiments of any kind which are not justified by the medical, dental or hospital treatment.
But aliens here are far different from any human opponent: they didn't make any demands, ignored all negotiation attempts and won't stop hostile activity unless killed or incapacitated. Aside from that, each alien doesn't show much intelligence on individual level, so it's not quite correct to treat them as "persons". The only sentient thing among them is XVI virus, but unless we are going to respect virus' right to infest and devour all living things on Earth, the alien invasion is much like a natural disaster and should be dealed with appropriately.
As for human morale damage - it's quite possible, as with each war. I remember the plot of the Incoming game series - in the first part you fought alien invasion as usual, but in Incoming 2 you took the side of some other alien race defending against humans, which became technologically advanced and xenophobic after the first war with aliens. Something similar could happen after the destruction of alien mothership here - not knowing if there are more XVI motherships or ET threats of other kind, having a number of unidentified XVI hosts on Earth which can form undercover common intelligence cells and provided with alien war technology, Earth goverments can unite under more totalitarian, suspicious and warlike one. In this case the final titles could show an armada of FTL ships being built on Earth orbit, saying "Now we must be prepared" or similar.