While I agree with what Hellbird said in relation to the reactivation and the implied indoctrination problem, I believe there should have been, as always, the neutral choice; Hand it over to the alliance. You've got to have some credibility with Admiral Hackett still. Why not call him over and deliver it to the alliance to study? If that were an option, I would take it.
It would have been a great piece to study, but I just don't trust Cerberus. The alliance wouldn't have the expertise to study it as well as Cerberus may have, but I'm fairly certain Hackett wouldn't pull the human supremacist shit on everyone.
In the third game, there could even be an extended subplot where the council trusts humanity LESS (if they're still kicking, or rather, eating doughnuts) now that they have obtained this potential galaxy threatening technology, furthering the theme of humanity working harder to save the galaxy while it's working harder to push them away.