I agree that the primary reason for deputising him in that position is to give him the chance to play in a role which fits his best characteristics as a midfielder. However, I don't agree that he is being put there because he would be marked out of the game in that Pirlo role. If there was a genuine concern about that, then I don't think the structure of the team would stay the same while Pirlo is absent from the starting XI. I don't really think coaches will look at the team and treat a 22 year old with the same deal of attention as they would Pirlo, because it's going to take a while for anyone to become as effective as him and earn that respect. Pogba has come into the role at a younger and more inexperienced level to Marrone and played the Pirlo role on his debut, I think Conte has assigned each starting player a substitute to be their replacement if the time is right.
It seems Pogba is being groomed for the Pirlo role (I think Raiola played his part in that), Giaccherini is hovering around midfield and deputising for Marchisio and Vidal while there is also Asamoah willing to fit into that position. Marrone becoming a defender/midfielder type, that Barcelona are so willing to produce these days. The shape of the team doesn't have to change this way either.
I'm not really fond of the thought of not using him in midfield at all though. I'm almost certain he can be more productive than Giaccherini (aside from distance covered per match) if he's given time in his natural role, and I don't like the thought of him losing a place in the team if he doesn't adapt to defence well enough. It's quite vicious really, in the few games he participated in last season he made a positive impression in almost all of them, and now he's required to adapt his game to a new position.