Similar to t-rav, I think the underlying notion that you make (and which I disagree with) is that there is a fundamental right to be admitted into Australia, and that this right can only be taken away in a trial with procedural due process et cetera.
This is nowhere near the current global consensus. If there is even a reasonable suspicion that you may be a national security risk, then it is only fair to deny entry. As long as it is limited to the few cases in which there is a real risk (and since we're only talking about fourty-six cases out of tens of thousands of arrivals by boat, I am willing to take a gambit and say there is a real security risk in this case) then I'm okay with them being denied entry en bloc.
Think of it this way. If I applied for a visa to get to Australia -- even a humanitarian visa -- there are thorough background checks. If I failed those - and there is no guarantee of any hearing, trial, due process or anything at all - then I would be denied the visa.
It's only fair the same procedure applies to those who arrive unauthorised by boat.