A time dilation device would be helpful, too. I know it was Sam who rigged the first one in SG1, but with the Pegasus Asguard and Rodney and the Replicators, I'm sure they could rig up something similar.
The Pegasus Replicators will be invaluable here. Even if they cant assimilate Unicron, they can help built a crapload of ZPMs and Atlantis-like ships. Also, is time travel an exploitable option here? Is there a point in Unicron's history that it would be possible to mess up to stop him from achieving the power he has, or even existing in the first place?