I liked this ep because it dealt with the serious flaws in Jack, especially as General. The last line about his hesitation will have to be further explored. But Jack's flaws are what make his character so great. He is complex. Just when you get comfortable with the character, there is a twist. RDA played Jack's frustration perfectly. Yes, he was punctuation in places and not the driving force, but there was powerful subtext there.
As to Daniel doing interrogation, considering the nature of the criminal, well, a soft approach may have been a better approach. Also, we don't see what went on before. Good cop bad cop. Just being stuck down that rat hole of a base with the prospect of being "disappeared" off world would frighten the hell out of me.
As to the Trust operations, I would have a better preparation if I were going to torch whole worlds of millions of folks. Not just a few guys with a few cans of stuff and a finite amount of launchers. So maybe TPTB are showing that the Trust is fallable and eventually will be defeated by its own limitations. It's like IRAQ, no endgame after you defeat a bunch of system lords, there are still others...Anubis is still running loose and one bad bad guy is not preferable to a whole bunch competing against each other.
And I thought O'Neill's last comment also indicated his ambivalence to free Jaffa. I mean, if they do ever get free, then what? They go running around the galaxy conquering other folks cuz that's what they do?