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.
Strawman. Nobody is arguing that there is a "fundamental right to be admitted into Australia". There is, however, a fundamental human right to seek asylum - i.e. temporarily admitted to Australia or an Australia-controlled territory for the purposes of a PROPER security/background screening. That is not what has happened here.
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.
If you'd read the article you'd know there was not a reasonable suspicion of national security risk that would have been proportionate to the length of detention.
"The State party (government) has not demonstrated that other, less intrusive, measures could not have achieved the same end of compliance with the State party's need to respond to the security risk that the adult authors (refugees) are said to represent," it said.
It also found that those held were "not informed of the specific risk attributed to each of them".
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.
This is a terrifying view, especially from someone who wants to study law, and I sincerely hope it comes from ignorance rather than informed belief. Due process and the rule of law are fundamental features of our legal system. For the record, immigrants are definitely able to appeal any failed background checks through multiple judicial channels, so I don't see why it should be different for refugees.