Yeah, get it, as a character it makes sense, but as a player you'd feel guilty. But you know, that's sort of what we should expect when we play as villains. You put the vest on her with the intention that it's suppose to kill her, and her life is in your hands. She's at your mercy. Her blood is already on your hands, and the fact of the matter is, there's no turning back now. The only, ONLY, way I can even imagine Serenity coming out of this not-dead is if she or Aria can somehow muster enough energy to create some sort of barrier around her skin but not the vest and let the vest explode. But either one of them has to figure out how to make the vest explode, which Serenity could try to tell Aria. But this relies that Jack doesn't react, and for just a moment, you let this happen. Because I've stated before, she's at your mercy. And now it's up to you to decide if you want to kill her or give her a chance.
Either that, or you retcon what Jack mentioned to Serenity as a bluff; that the Shadow Complex doesn't need her alive. Because that way her life becomes important, and the bomb merely being a very real threat but also a deterrence from making her make another escape.
Alternatively, you let me coming in as Dark Matter, find Serenity, see the vest, consume the vest to break it down into raw materials and to make it inert. I could have Dark Matter do this, and he could do it in a short time, operating on nothing but gut feeling and a lot of luck. But I'm not going to do that as it does seem rather convenient to the point that, given that I just now thought of the perfect way to solve this disaster, it's practically divine intervention, so only if you let me.
You took the job, pulled the trigger, set the bombs, and now you got to live with the consequences. If you really want me to tell you what to do, I vote that you let go of the deadman switch and let what happens, happen.
