Although it's hard to know what's in the mind of the screenwriter, all evidence points to the first conclusion, that Gideon is just a creepy weirdo who's spent far too long working in isolation watching murders on the telly-screen and who likes to make vaguely prophetic statements to his colleagues.
In the earlier versions of the script and the source novella his character simply doesn't appear at all. Much of his actions are ascribed to an obsessive-compulsive character called Ennis Page who takes care of the precogs and manages the computers recording the various precrimes detected. Tellingly, Ennis is clueless about the way in which his boss has duped the system (in this case by creating a fake precog disk and simply placing it into the outgoing mail slot while Page is otherwise distracted).
If we assume that Gideon is an analogue of Page then we can presume that he was similarly clueless:
LISA (CONT’D) : Somebody tried to frame him with a fake. And somehow it all became real. Why, Ennis? How could this happen?
Ennis gives her a look that’s on the other side of comprehension.
LISA (CONT’D) : You handle the discs. How did a fake one get delivered?
Ennis’s eyes roll back into his head.
PAGE : Coffee ...
LISA (CONT’D) : You want-- ?
PAGE : He spilled coffee everywhere ... Everywhere ...
LISA : What coffee? What are you -- ?
But Ennis sags unconscious. She shakes him hard, even slaps him, but
Ennis is out. She lets him drop down on the sofa.