If Daniel (and the Carter and Teal'c to a lesser extent) couldn't put their own personal feelings aside and see that Jack had done what had to be done for the sake of catching the members of the rogue team and helping restore balance within the allies, then they shouldn't be on the team.
What I would have like to have seen at the end would have been Daniel confessing that he never really "bought" Jack going rogue/that he knew something was up, but played along for Jack's sake. There have been some fan fics along these line; very well written.
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