The Blind Sheik was tried in Federal court and convicted and now serving life in a North Carolina prison. Different circumstances, since he was living in New York and fairly easy to grab up, while al Awalaki had moved to Yemen. Another terrorist who got his day in court was 9/11 plotter Zacarias Moussaoui, who's serving 6 life terms in the supermax prison in Colorado. But Bush didn't think the men we captured in Afghanistan should be treated as POWs under the Geneva Conventions (even though they served what was then the recognized government) or as criminal terrorists, and so we have our little slice of the gulag in Cuba, with the only way out for them being death.
How would sending in a SEAL team to assassinate him differ from a drone strike? My point is that at its base, either method is extrajudicial execution, and the only difference between bin Laden and al Awalaki is that bin Laden wasn't an American citizen. And that's what got the hearts of Constitutional "scholars" bleeding all over the place -- that and the fact that Obama OK'd the strike. They have no problem drone-bombing every Bedouin from the Mediterranean to the Black Sea, but al Awalaki had rights, never mind that there was no practical way of ensuring due process for him.
Bergdahl might get off if the military judge buys the defense's assertion that Trump's campaign comments calling him a dirty rotten traitor constitute undue command influence. It's an odd case, even the investigating officer said that prison wouldn't be appropriate.
As for Manning, he wasn't pardoned, Obama just commuted his sentence. A pardon wipes the conviction off the books, and Obama wasn't going to take that step. The commutation just means he gets to leave prison early -- he's still a convicted felon with a dishonorable discharge, which closes a long list of doors to future employment. But no doubt some ultra-liberal entity will take care of him.