I think it's just as minor an issue as burning the flag. I see your point though, the constitution is a symbolic representation of the ideals, values and customs of the Australian way of life, just as burning a flag would be seen as an attack upon said ideas.
I believe that, throughout history, great change has resulted through protest. The French Revolution, Black Marches on Washington, The Eureka Stockade (to give an Australian example). Everyone of the protests we learn about that have occured throughout history are, in a way, attacking the values and ideals of a nation. King's "I Have A Dream" speech does it in a very eloquent fashion, I admit, but it was a protest none the less.
Personally, I would rather live in a society where the burning of flags and constitutions is the way to protest against a Government or authoratitive body. If it's not the flag being burnt, chances are it's the people. And that's slightly worse, if a little less symbolic.
I admit this particular issue is a delicate one, but surely blown out of proportion. For me, it became an offensive issue when he was offered the chance to carry the Australian Flag in an Anzac parade - an honour surely reserved for a deserving, high achieving Australian; not one who gained notoriety after a media circus and some matches.