I hope so! Sebastian was probably my favourite companion in the second game. The character himself had three possible fates/endings while most characters only came with two or so. I liked Anders, too, so Sebastian made the ending very interesting. Needless to say, Anders did not always survive anymore.
While I leave headcanons to the actual owners of the story, I still have some wishful thinking & hoping regarding Sebastian.
I like to think that should you spare Anders, a vengeful Sebastian would have dared to take more drastic actions in reclaiming Starkhaven and would already have managed it. We'd hear about the attack on Kirkwall if nothing else.
A rivaled Sebastian, lacking a deeper goal, would still be in progress of reclaiming the throne. I really have no idea how we'd even meet or hear of him without visiting Starkhaven itself. We probably wouldn't.
And finally the friendly Sebastian, who vowed to become a brother in a Chantry. I believe the world is in too great of a turmoil for him to actually become just a brother. I hope someone would have noticed his skills and he would have been made into a similar Chantry agent as Leliana is. Maybe the two would even team up.
But as I said, just wishful thinking.