Thor actually has examples of explicitly stating he holds back most of the time, even against physical "peers", and even if it meant defeat.
Spidey developed his own "World of Cardboard" syndrome when he beat Sin Eater so badly, he left him crippled for life, and was given a detailed rundown of his shot nerves, broken spine, punctured organs.. I doubt he could stop holding back against a street leveler any more then Superman could against everybody else.
But the main point, is no hero who normally holds back is going all out against another hero. Even Wolverine won't try and kill, say, Capain America or Spidey, regardless of his willingness to kill villains.
Just because Cap was told not to hold back, doesn't mean he was hitting Superman as hard as he could and risk killing him.