1. They are showing remorse...and they will show it more. Mr. Black, as you will find out, is the Chief Tactical Officer of the Trust, and a former Ranger. He heads up security and whatnot, and his personality is such that he's going to be more jaded about these things that pretty much anyone else there. The Trust employs lots of Superheroes. He's not really one of them. Ms. White, otoh, IS really upset about it, and I can show her and others making a bigger deal about it if that helps.
-- That probably would help some...it would at least suggest that they care about the lives wasted in their tests.
2. They did not know about the other two supers, and because they did not know about the technopath. they did not know that passing aircraft would be at risk.
-- But they knew about the others. And they knew about us. Part of what I'm getting at is that it's exactly because of these unknown factors that tests are NOT done like this. Any group that valued life would take all precautions they could...test or otherwise...to see to it that any risk that was present was as contained and manageable as possible -before throwing anyone into it-. To do otherwise suggests criminal negligence. If they can't control the situation, then they needed to relocate the test to a situation they could control.
3. "Just" drug smugglers. You'll see. What you broke up was worse than it looked.
-- What they were doing there doesn't change any of the substance of my observations. If it was so important that these people be stopped, it could have been a first official assignment, and us sent in under conditions as optimal as they could make.
4. The resources the Trust provides and the urgency of the leads that come from what you guys gathered may prove enough to work with them, even reluctantly. Thess will also have the added incentive of learning from a much more experienced white witch (...and how bad could she possibly be if she can channel so much white magic)
-- Their resources clearly weren't useful in the "test."

And the urgency might lead us to work together, but why include the Trust? As for learning magic...there might be temptation, but I don't know if it would be enough. She's come this far on her own after all. And Ms White might be a shiny-good-great person...that doesn't make the Trust a good employer.
I feel a need to explain here. Because now I am afraid it's going to look like I'm just being obstructionist. I'm really not. I just don't think the core problems have been addressed...except perhaps the remorse thing, which really isn't the main problem. Seriously though. Put yourself in the shoes of these characters. They left their living rooms, got in a van, and under false pretenses were thrown unprepared into a potentially lethal situation where they were shot, burned, exposed to toxins, blown up, smashed, smacked, beaten into a bloody mess in some cases...and now...hey! It was a test! Yay, you passed!
How can we not break our #2 pencils and tell them what to go do with their damn test?

Because not only were we put through hell, and under artificially bad conditions...ie not only did the Trust not try to make a hard situation any easier, they actually went out of their way to make it more difficult...but we were put through hell -on purpose-. And the thought that a boat full of additional supers, men with super-killing weapons, and high explosives could come onto the scene without the Trust knowing it doesn't really help much. Sort of like a certain Presidency (which shall remain nameless to conform with posting guidelines

) the question becomes...are you evil, or just incompetent?
------
But that's just a rehash of points already made. I turn instead to possible solutions.
1) THE MOLE: Turns out someone in The Trust can't be trusted. They heard about a batch of new recruits and threw a few monkeywrenches into the game. Only problem is...we lived. When the contacts we were supposed to meet hear about what happened in detail, they'll realize that the training program we were supposed to have encountered was something entirely different and more deadly. Tracking down and finding this mole could become a mission later on.
2) THE PURGE: The Trust is split within by internal factions...ex-special forces paramilitary types that formed the program in the first place, and a newer crop of supers who have gradually been asserting more power. The scandal this recruiting technique causes within the group provides the newer faction with the power it needs to start some major housecleaning, starting with the ones in charge of recruiting. These purged individuals might then form their own group of highly trained, highly equipped nonsupers that have a deep rivalry with the new Trust, and chips on their shoulders.
3) THE HEEL-CLICK: This was a Matrix-like brain sim/magical collective hallucination or something. Retcon ensues. Kind of icky, but it gets the job done, and no hard feelings.
4) THE WILD REBELS: (crunchy, chewy rebels) In what would probably be a 360 degree departure from everything you have planned, the PC's decide not to go with the Trust, but still team up. Requires a change in title. Probably negates anywhere from 1/2 to 3/4's of the reason you wanted to run this game in the first place. Least attractive option.
Open to other ideas too! This is just to get us started.