Mmm, I read it as, well, to separate it, (1) the fic itself being aware of the dodgy things underlying Tony Stark/Iron Man and that canon's worldview, and (2) Hardison being aware ditto (poor thing, when he's a step behind the others in realizing the problem with Extremis's mission statement, but he learns fast). And I expect the _Leverage_ team to share his views. So I think I take a more optimistic view of the ending than you, as my comment there may've suggested.

(And now I *desperately* want to see the team fix Tony all the way. With Pepper.)