Del Piero was dropped out of the first team long before we changed to 4-3-3. To be precise, 3 matches before we changed to 4-3-3.
But after we changed to 4-3-3 Del Piero became even less needed, at least in that formation since there is little space for him to play there, unlike in a 4-4-2.
So yes, Agnelli's comments of course, but the formation change is also a reason why he started getting less and less playing time.
P.S: Check Krasic too. He too started playing less (or better: none) minutes after the formation change. Actually, it goes for all the wingers bar Pepe. They would have gotten more playing time in 4-4-2 than in 4-3-3. And they all did get more playing time in 4-4-2 than they do in 4-3-3 with Vidal, Pirlo and Marchisio all available. Without Agnelli announcing anything about them.