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I think the important thing here is how it affects the result.
Remember Wiggins waiting for Cadel, after sabatage saw him puncture repeatedly. Thats was OK in everyones book. But as Cadel was a firm GC contender. Him not losing time affects Things.
Basically -
Helping riders of a different team not lose time because of mechanicals = good.
Helping riders of a different team win time despite mechanicals = bad.
So having thought about this a bit more, and not finding myself able to get as angry as everyone else on the internet (twitter) seems to be, some non-loaded, serious, questions:
What should have happened. No penalty? What if Porte were to win by 1 second at the end of the race? He would have lost more than that without the wheel.
What if Aru had punctured and a fellow Italian from a different team had swapped wheels allowing Aru to save time he would have otherwise have lost (to Porte), followed by him saying "We Italians help each other out" (imagine Mario accent). Fair play or would the Anglophones be chanting "conspiracy!"? And if Aru won on top of that?
It seems that sharing wheels when it doesn't really impact the results (as AndyP said above) is all good, but this is a situation where it does matter. He's a contender.
I honestly don't know what should have happened. I'm just gutted Porte is so far back now, but hopefully it will encourage him to go out on the attack and make for an even more exciting race.