According to Elidibus, he had been "away" for some time until our encounter with him in 2.1, likely on one of the Shard Worlds. Logically, that would mean it was impossible for Gaius to have dealt with him.

There's no evidence to suggest the Griffin is working closely with Elidibus. All we know at this point is that he was aware of the Warriors of Darkness and Elidibus' plans for them.