I think the problem is the terminology of a "super profits" tax. It is reasonable to charge a "resources tax" above the bond rate because companies are exploiting resources that belong to all of us.
But call it a "super profits tax" and you look stupid charging it for any profits above the bond rate, as obviously you should use a cost of capital.
So, Rudd has messed up there.
The current royalty system include tonnage royalties ($5 per tonne for example) or revenue royalties (10% of revenue for example). The former takes no account of price received, the latter of costs incurred so the move to a profits tax makes sense.
Personally, I think the bond rate is fine to use as the benchmark below which nothing is payable (as long as you do not call it a super profits tax, DOH). The issue is then the rate at which the tax is paid and the Government appears to have gone a little too high. And, they should have gone ahead with other reforms on property taxes and stopping the high income earners super rort