I feel like Sharlayan's public motives for abandoning the colony are their primary ones; maybe Sharlayan had some secret ulterior motives but I have to assume they're secondary. Firstly, the evacuation was something that was planned out for a long time; you have to remember that they basically abandoned the colony literally overnight, it wasn't something that just happened. Secondly, they did make serious attempts at trying to court Garlemald for peace/neutrality and we've seen they aren't completely opposed to the idea as shown by countries like Radz-at-Han and Koshu who maintain their independence despite being located very closely to Garlean-controlled territories. Finally, and most importantly to me, they allowed people to remain behind in the evacuation if they wished to. We've seen that Sharlayan can have an extremely strict laws imposed on their citizens and are not unwilling to assassinate or torture their own citizens to ensure that they follow their perceived ideals; while it could be argued that this is just an extremist faction with the country, we know that this group does have seating within the forum empowering it. For this reason, I cannot imagine them allowing someone like Matoya, who is both a powerful and knowledgeable individual and was a frequent critic of the Sharlayan forum to stay in the ruins of the colony for years following the evacuation if they were trying to cover something up there.