Just by the position of the systems the GTA (and the Vasudans) end up colonizing, odds are that colonies will be in the line of military operations. History suggests neither side is likely to draw a sharp line between military targets and civilian shipping, and since the strategic and ideological objectives of both parties include land grabbing, colonists will probably be treated as fair game for raiding and anti-merchant work, if not necessarily full-scale nuclear attacks.
Most civilian casualties would come from disruptions in the colonization program caused by military events: starvation, ecosystem collapse, interruptions of supply, untreated epidemics. The colony program is quite rapid and the sheer number of human beings that need to be moved to achieve FS2 population numbers is colossal.
There's also the question of the species gap. Human psychology, at least, will make it fairly easy to sanction mass killings of Vasudan civilians.