Maybe. The thing is they have been pretty open that its the Garleans we will be fighting in 4.0. Garlemald is the powerful unyielding powerhouse which is what makes it impressive. Yeah it has disasters, setbacks and losses but is such a large, powerful and tenacious enemy that it will regroup, adapt and return again. A faction of the resistance doesn't strike me as a really effective threat to that, even if they are desperate. That said, I am certain we will have conflict with the more extreme elements of the resistance.
I think that when we ally with Garlemald, at least at first, it will be against the only power outside the Ascians on Hydaelyn that can pose a real threat to Garlemald, Garlemald itself. I think somehow the events of Stormblood are going to lead to a major power struggle in Garlemald and we are going to be dragged right into the heart of that. That I think will be in 5.0 and I think Zenos will very much act as the wick to start that fire.
Edit post Live Letter:
Ok scratch that. I have no idea why we are heading to Ala Mhigo. I thought the dungeons might give a hint.