If Thancred can miraculously be rescued from Lahabrea's direct possession then I'm sure the story could move in a direction where Varis is freed from the manipulative clutches of scheming Ascians.

It's reasonable to assume that Varis is due to meet up with Alphinaud on at least one more occasion based on their prior conversation and the direction Alphinaud is headed in.

Perhaps Varis will find himself overthrown and forced into exile, or imprisoned. There's a lot of interesting things that could be done with him - and previous titles have explored similar themes, so it's safe to assume that FFXIV isn't going to shy away from them.