Look, collusion happens. A lot. People make alliances in races, and friendships are forged by riders across teams. Tiralongo and Contador is only one example. Something like this is one of the only ways they're actively able to enforce limitations on it. After all, Tiralongo could argue (implausibly) that he would beat Contador in a sprint and the break needed extra legs, therefore it's in his interest to carry him to the front and work together. Unrealistic, sure, but feasible.
If back then Contador had punctured, Tira had given up his wheel and Contador had rode off into the sunset... how many of you would have been irate if Alberto HADN'T been given the two minutes? Part of it is that this was an expected GC-irrelevant stage, so it doesn't seem like anything major has happened and it's just a nice gesture from Clarke rather than any real collusion. But the rule is there to prevent this kind of assistance affecting the GC. Ironically, the subsequent application of the rule has affected the GC more than the assistance did.