He's called the "only sane superhero" by Reed, who is himself portrayed in a deeply unflattering light so that doesn't exactly rate as a ringing endorsement. Peter calls Reed out for his coldness and lack of humanity so it's not like Dzarsky is having someone above reproach speak to Cap's heroism and Tony's lack thereof.
Peter's own feelings towards the war aren't clear. If anything, he seems more inclined to be on Tony's side in wondering whether it's his responsibility to use his powers to affect an end to the war.
The basis on which you think it's shitty writing is so absurd (characters are complicated and the lines between right and wrong aren't always clear = character assassination) that, I agree, it's not worth discussing.