This is a lot to respond to all at once, but I'll just take on the first article for now
The subject of the article admitted to delivering the explosives that killed innocent people.
He admitted to attending an AQ training cap for "self defense purposes".
He also admitted to helping AQ operatives obtain fake passports and cross boarders illegally.
Doesn't sound like much of a problem to me to hold him indefinitely.
From the article you linked:
"Ghailani, a Tanzanian, is suspected of buying the Nissan truck used to deliver the bomb, supplying the TNT and detonators, and later running a document forgery office for Al Qaeda in Afghanistan. He was arrested after a gunbattle in Gujrat in eastern Pakistan in July 2004."
In his own words: "At times speaking in English, Ghailani said he went to an al-Qaida training camp in Afghanistan after the bombing, because he wanted military training for self-defense."
Again his words:"Ghailani said he later he worked for Al Qaeda in Pakistan providing passports and documents to help them get across borders"
I'm not feeling too bad for this guy if he knowingly worked with a known terror organization and then later admitted it, and now regrets it because he is locked up.