You mean the guy that spent about 7 years utterly divided between God and country? The one that seemed to be the only companion that lacked any conviction? Say what you want about the rest of the crew, but all of them had beliefs (for better and for worse) that they truly stuck to. Sebastian seems to lack a real personality, and that isn't on the writers. I think that was the point: To show someone so torn between two ideals that his own identity is in free-fall.
That being said, his threat is utterly empty. By the time he secures his throne, regains trust of the people, and trains/builds his army up, Anders will be long gone (either dead or out of the Free Marches.) There really wouldn't be a point to attacking Kirkwall, and hopefully Seb has grown up enough by now to realize that. I really do think it'll take awhile for Sebastian to get all of that going. A fair estimation (at least I'd think so,) depending upon the strength of his advisers, army, economy and allies, would be about 3-4 years before the kingdom would be stable enough for an attack on another Free City.
Remember, there was a puppet king on the throne in Starkhaven during DA2, a distant cousin of Sebastian's that was placed there by his family's enemies. Even Seb (who's normally pretty patient) called him an idiot. A lot of rulers like that tend to have a lot of "trusted advisers" that would be happy to funnel the royal funds towards their own personal gains. Or those rulers are just extravagant spenders themselves That could be a real economic disaster and one that would certainly take some time to clean up. I figure that, by the time his kingdom is stable, (about 9:41 Dragon or so,) he's going to have much bigger problems.
He's not a violent man, and he said those things in the heat of the moment. Once the reality of retaking his throne sets in, he'll calm down. His kingdom should come before any petty revenge. With the Breach, he strikes me as the type to protect his people rather than trying to track one apostate all over Thedas. Assuming of course that the player left Anders alive.
Oh and before anyone asks, no, I don't like the character. However, I was trying to be fair here. 