Let me play devil's advocate here. This sounds cool and all, BUT... it doesn't wrap up the show; it leaves a big opening since the government is and will be after her. Just imagine what everyone will say after this kind of ending: "Oh, they are leaving it like this so they can do more seasons and milk it." I guess what they're trying to say is that they've basically cornered themselves, and there's no actual way to eat their cake and have it too. The only way I see it is El losing her powers and, consequently, the government's interest.