So, Superman has taken all Thor could give, THEN took multiple hits from Iron Man AND Wonder Man. That is a hell of a better showing than Thor.
If hitting him on the ground isn't desperation, I don't know what is. Superman took down their highest card, of course they don't want him getting up. Superman is ready to get up, Thor is done, he can't/won't get up - maybe he's in shock, whatever. You are trying to make excuses for him, but Superman is clearly ready to get on his feet quicker than Thor. Thor even tries to save face, by saying IF Superman can fight, he will too.
Regarding Doomsday, are you saying Superman looking over Thor's unconscious body (in case you hadn't realised that) was tougher than him getting killed by Doomsday. Does this fit your definition of Thor being 'clearly' tougher?
If Thor’s hammer shot had landed, the situation would have been reversed and it would have taken multiple shots from the JLA to bring Thor down. Thor’s mistake was bravado. He chose to run through the heat vision as opposed to blocking it and that added to his wear.
Doomsday was killed by Superman’s final shot whereas Thor is temporarily KOed from the final shot of a Superman who is stronger than he was in DoS. So it does fit with what Superman clearly states. We do actually see Thor send Doomsday flying.
As you can see in the scan, Thor is already in a sitting position while Superman is being helped off of the ground. This indicates that Thor was up earlier.