If not subspace, then what else? Another alien race? the Vasudans? We've already made friends with them. Considering that the FS1 ref bible leaves open the cause of the T-V War for sci-fi writers, I don't think that there was any plot-critical or sinister reason behind the start of the war, which probably means that the Vasudans aren't interested in killing us. Besides, they're portrayed as such peaceful wise historian types, even the HoL.
People forget that the game is named "FreeSpace". That's Subspace, before they changed the name. So why else would they name the game "Subspace"?