The Order is basically the pinnacle of human technology.
They have a network around Sirius, and they have nearly limitless resources.
The Core also has nearly limitless resources.
I'd have to side with the Core actually becoming infested and then going to war with the Order more avidly than before.
In the ensuing war, they'd probably tear each other to pieces and rip the Omicrons to pieces in the process of doing so. It would take ages, but the Order would probably survive after the destruction of the Core and the destruction of most of the Order (and probably the destruction of Omicron Minor with the Core/Nomad fleets) in some small form and rebuild the Order - though I'm not sure if the Nomads would be too powerful by then or not.
