Okay. I've slept on it, and I think I see how it can all work...at least for me.
Basically, first of all, the Trust's official position on the matter can't be represented by that one guy who basically tried to blame it all on the victim.

I realize Spirit acted recklessly, but one big reason she did was because we needed info (which she was trying to get) and because she didn't believe there was any threat (we had no reason to suspect any supers, let alone supers with such specific abilities). If this had been a sanctioned mission, we would have been told at least enough to make us more cautious. So there needs to be some recognition, officially, that at least SOME of the responsibility is borne by the Trust, and some actual apology/remorse for that and for putting all our lives in unnecessary danger would be nice too.
Secondly, there needs to be a debriefing that explains what happened. On review of the details, I find that the Trust -thought- they had this under control. They were prepared to intervene, if necessary. They believed the risks were manageable. The appearance of these other supers disrupted that control (though admittedly, the moment that control was disrupted, the logical thing to do would have been to intervene immediately...but oh well

). Since one of the unexpected supers was this tech-controller, perhaps they can discover that he was able to subvert Trust tech to avoid detection...an unexpected eventuality. Furthermore, the Trust operative that made the decision not to intervene when they realized things were getting out of hand could be reprimanded (thus giving us an NPC to focus our dislike upon, while exonerating the organization as a whole).
And finally, a good demonstration of what the Trust can offer a team of superheroes that they couldn't easily provide for themselves. A briefcase of equipment won't really qualify.

The most valuable commodity would probably be information on criminal activities and supervillains, headquarter facilities, access to super-level training and so on that can justify exp spending on powers and such.
Oh, and some kind of assurance...verbal's fine, doesn't have to go into detail...that they're making changes to prevent this sort of thing from happening again would be good.
Edit - And oh yeah, don't retcon the death unless you're willing to 'make it all a dream.' Especially since in some ways, the problem isn't specifically Spirit's death, it's how the bad situation led TO her death. Just making her life won't fix that.