Warning: I'm writing this after my first skim of the post. I will edit this accordingly if I realize I'm wrong after more careful analysis.
Garlemald didn't know what Nael was doing. As far as they were concerned, he was going to drop a space rock on Eorzea and save a metric ton of military strategy and paperwork.

Meanwhile, in Garlemald...
Gaius suspected what he was doing, but wasn't able to conclusively prove it until he observed it first hand from his position "on high" at the Battle of Cartenau.
Therefore, I don't think he has a change of heart at all - I think he's more confident than ever that he's the only one who truly understands "the truth." I think Nael's last words are that he pities the foolishness of The Empire for having a vision so much less than his own that they never even realized his true intentions. All they care about is the conquest of Eorzea and eradication of the Primals, whereas he understands the existence of the Mother Crystal and the goals of the ancient Allag.
This is a very rudimentary analysis, of course, because I've been doing the storylines in order and I have to get through the three intro scenarios in order to do the main scenario so I can do the Seventh Umbral Era scenarios... which is why it's so important that we tackle Lominsa as hard as possible as soon as possible ... so, uh, please accept this IOU for a full analysis of van Darnus at some point.
</em winces>
Please look forward to it? /ashamed
EDIT: Alright, you got me, hold on. It's time for a Lominsa break for a few minutes. I'm gonna do a YouTube playthrough of the Seventh Umbral Era and see what I come up with.