...i will not comment on that games>books thing. Just this: if the books weren't canon, what should we know about the Halo Universe? Think about it. Try to make logical connections between the games, without reading the books.
Anyway: 343 Guilty Spark, the Monitor of Installation 04, is....DEAD. *thunders and lightnings*
343 Guilty Spark, the original one, wich basically is ////////SPOILERS\\\\\\\\ Chakas, it's still alive, and at the end of Primordium we know that he has taken controll of a Human vessel, a scientific one.
Now, we can analyze the informations received from that last chapter:
-we don't know it's name. It might actually not be the Infinity.
-it is said that the vessel broke the formation with the fleet, departing from it's original destination. (note: FLEET)
-the Captain (unknown) was talking to him. (so, he knew 343 would take command of the ship?)
-343 stated that "one of my incarnations gave you problems..." or something like that. "One of my".
Take your conclusions.