I am also currently at that mission.
First i lost 3 Ships and i got that "we lost a lot of people because we didnt do our job" talk and i understood him, so i tried again and this time i just lost 1 ship close to the end and i got the same complain from my Wing Leader. Now that i personaly find odd in that mission.
I mean we are at war, till this point in the game we lost already about what 20+ Capital Ships (counting does against the player could do nothing about), and now that guy complains to me about not doing my job because at a head on attack on a Kilrathi fortified planet, who throw tons of bombers (the ratio between enemy bombers and enemy fighters isnt really fun in that mission, but oh well) and anti capital missles at us, we lose 1 ship??? What does that guy expect? if all strikes would go like this than we would not be loosing the war.
Considering the situation i would say the pilots have done a awesome job that only 1 ship was destroyed. Normaly the whole fleet had should been pulverized.
At this outcome, losing 1 ship, he should have more said something like "its a shame about the 1 ship that was lost, but thanks to you all this day didnt see more casulties"
Just my opinion.