Was it? he's being chased by the Shogun, he isnt going to fight them, they are still his people they just didnt like the way he dishonourably dispatched the Mongols but in that time he did what he had to do. So what is a sequel going to be? pure stealth trying to avoid all Shogun contact? I dont think that would make a very exciting game.
The second game was always going to be a different Ghost, Jin's story is done, we already knew this. Now whether they could have done a story based around another character from Tsushima for the second Mongol invasion, then, maybe? but people would still whinge its not Jin. Think of the Ghost as just telling stories of unknown (fantasy) hero's of Japan, it's not really that much different to Assassins Creed in that respect which is perfectly fine as far as I am concerned as it means we do get to visit different places, different time periods, different enemies, it keeps the game fresh. (and how could this possibly tread the same narrative as Tsushima? different protag, different time period, different part of Japan, different enemy as I previously said)
There is nothing stopping them from jumping around time periods so they could go back to Tsushima at some point (probably not though, not a lot to say there)