Do we know that Gemini *was* a 'backwater' sector in the Nephilim War? It's implied that Perry Naval Base was destroyed--it may have been a major battlefield.
From my compiled post-Prophecy Timeline:
"2685 - Over forty systems scattered throughout the Sol, Vega, Trk’Pahn, and Gemini sectors are quarantined and blockaded by a coalition of official Confederation and conscripted local militia vessels. Supplies are delivered to the afflicted areas with unmanned drones. (POL2)"
"2686 - The Gemini Sector is the hardest hit by the virus due in part to the pirate and mercenary activity that has distributed contraband alien technology. All jump points out of the sector are blockaded. Drone transports are utilized to send supplies to systems. (POL2)"
"2688 - Mass inoculation against the Nephilim Virus begins in earnest.Emergency teams are sent to key junction systems within Gemini to evaluate the damage and assist survivors. The economic and social impact involved with the loss of Gemini’s cultural and industrial resources forces the CCSP to reevaluate its strategy for the pioneering effort."
So three big things:
1) A blockade operation was going on, so there were likely to be lots of ships in the area. There are ALOT of jump points leading into and out of Gemini, so it wouldn't be a small thing to shut down an entire sector.
2) The Nephilim obviously felt the system was significant enough to the war effort that they clamped the whole thing down with a Virus. Not likely something they would do to a backwater sector.
3) While we have the reference to a 'hulk' we also say that the 'weapon of mass destruction' must be disposed of. So here is an alternate theories: maybe the ship is still 100% intact and operational...but sometime during it's enforcement of the quarantine it got infected, and now it has to be destroyed because of the infection. Thereby neatly skipping the need for Gemini to be anything like a front line sector and maintaining it's backwater standing.