Regarding your question about the premise/blurb, I think it lacks a bit in focus. You give out a lot of details that aren't really relevant for luring in readers, and which kinda clash with what you're saying about it being a superhero story. It sounds more like a spy thriller kind of thing? 
I know from experience how hard it is to cut back on information for the blurb, as I am especially BAD at this. XD But I think it could benefit from first figuring out for yourself what the theme is, in the end.
Which brings me to your original question: power or no power?
The way I see your premise now, it feels as if developing your MC into a person who abhors this organization could lead to an interesting moral conflict if the finds out that he NEEDS exactly their powers to help his friend. What is the price of this power? That question leaps at me when I look at your premise. What price is he willing to pay? What drawbacks does it bring?
One of the most poignant sentences to date from superhero stories, for me, is: "With great power comes great responsibility." But great power also always comes with a price, so maybe that is something you could expand on?
As @tired_programmer already said, however, that kinda depends on your story. Again, your theme. Guess you have some figuring out to do? 