It's an interesting idea for a CG, but it would have to be carefully crafted so-as not to impact the story or direction of the game. For example, this CG would lead towards Maia becoming inaccessible or the destruction of all human stations and settlements upon a successful Thargoid invasion. I don't think FDev wants to change Obsidian Orbital into Obsidian Memorial as you don't want to upset his ant hill followers
The CGs will have to be more on the sidelines of the state of affairs. Supportive tasks that if failed, would not create a ripple that could lead to massive changes. There may be some unimportant systems lost or gained in some conflicts, but ultimately FDev needs to maintain a stalemate between the two warring species to keep the content and current state of affairs accessible to everyone.
With that said, I can see CGs in the following area:
1. Conflict zone CGs that will significantly reduce stability in the system if the conflict was lost to the Thargoids (famine, outbreaks, lawlessness). So in a way, you're fighting to keep stability in the system.
2. Supply missions to keep the war effort fueled. Food, clothing, weapons. Since these commodities pale in comparison to trading gold, FDev will need to incentivize players to complete the objective. Perhaps reward war bonds for a monetary boost per delivery (similar to Edmund Mahon's powerplay special) instead of giving a flat cash reward at the end. This would be a good way to shake up the reward structure in CGs too.
3. Research CGs can also be given, but if the fail they shouldn't have an impact on the game. Things like you need to research XYZ in order to unlock necessary weapons ABC to successfully attack Thargoids. Instead, such research missions might help reduce costs of said weapons instead. Finding cheaper ways to make them, for example.
4. Bounty hunting missions against pirates exploiting the warring states. Not a whole lot of creativity here, but it's an excuse to have a bounty hunting CG every once in a while since bounty hunting against Thargoids doesn't make sense.
5. Invasion missions. This would be extended on Thargoid Conflict Zones, except it would involve planetary invasions. We haven't seen these before and it would have to be implemented by FDev (ie: pipe dream talk right now), but it would be really cool to see fleets pull in and shoot down bases and structures. To have combat SRVs go in and take down ground units (currently only scavengers) and successfully invade / conquer ground bases. Again, pipe dream, but just replace combat with research and fetch missions and.., well there you go.
So yeah, that's my take. I think Galnet will piece together the main plot and FDev will try to shuffle things around to make it relatively engaging. CGs will be there on the sidelines to give commanders some indirect influence over the story.