Collective morality
In the same way that Muslims flying planes into our buildings is not a collective condemnation of all Muslims, neither do the immoral actions of some soldiers reflect the morality of all of them. And it certainly does not nullify the moral argument for the war (which can be argued as a completely separate matter.)
Certainly there were Allied atrocities in WWII. Did this make the defense of freedom against fascism immoral? Or just those who acted immorally?
There are those who point to the prison pictures and go, "this is our military," or "this is what the war means," or even worse, "this is America." That's all a load of crap.