Well, I thought it was pretty clear that Gaius was speaking about killing the Ascians. It did show Shadowhunter right after the line after all. And we've already established that he's most likely out to kill the Ascians given that he's lugging around Ascian masks and talks about getting rid of an infestation and everything. We don't know where exactly he'll land on the good guy to bad guy scale, although given they made his reign over Ala Migho seem a little nicer in Stormblood I wouldn't be surprised if it's the former.