Honestly, looking over the story idea again, this is where everything kind of breaks down, because unless you're having the Batarians bamf from somewhere in their occupation zone, they're going to have to trek through the Combine and Terran corridor to get to Terra. Unless ComStar/Word of Blake/Shadow Broker gave them nav data that pointed out rarely used systems to travel through, it seems really unlikely that the Batarians would be able to get to Terra undetected.
Also, speaking of ComStar/WOB, what ever happened to them in this timeline?