Well, I'll have to go home and take the book out and read the Ponder bit again. But, if I remember correctly: Ponder did not get involved at all in the training of the team, he delegated the whole thing to Nutt, when the team was first formed. So he had next to no experience at all when, in the absence of Nutt, he had to take over the training. And, even if he is younger, more practical and into new and modern things, first and foremost, he is a wizard and, as such, thinks that walking down the stairs to the dining room constitutes healthy, invigorating exercise and just the thing to work up an appetite. The only person remotely into sports in that university is Ridcully, and I suspect that's where the "running on the spot" idea came from - Ponder must have seen him doing that someday (when the character Ridcully was first introduced, we were told that he was in the habit of jogging in the morning, as well as shooting every blessed thing that ventured within range) and thought, as a complete outsider might, that this must be sports, sure enough.
As for the way the scene runs - well, it's Pratchett! We expect a belly laugh now and again! We hope and wait for it, and we laugh at the expense of most of the characters - Ridcully, the Dean, the Senior Wrangler, Macarona, that Music Professor, whatshisname, almost everyone from the University, as a matter of fact. It doesn't mean that we don't respect them. Why should Ponder be an exception? I certainly have respect for Ridcully, and - you remember in Night Watch, I think it was, a scene where Ridcully gets blown out of his building when in his bath, and lands outside still in the bathtub, wearing nothing but his hat, and there are all those people present, and he stands up, not realizing that he is naked, and refuses to listen when someone points out this fact, declaring that if a wizard has his hat on, that is all the attire he needs? Getting ridiculed is the lot of a Pratchett character. It's all in good fun.