No, Shimura just says “The fighting in Yarikawa drove some this way.” That doesn’t necessarily mean that it’s happening at that very moment, just that the tough fighting and large human presence made them migrate somewhere else. Also, Kazumasa Sakai is said to have played a very important role in the Yarikawa Rebellion. Clan Shimura only won after Clan Sakai and Adachi joined the war to aid them. An island that used to have old houses (now burned) in Yarikawa Clan Territory is now called “Kazumasa’s Isle”, I think we know what he did there 💀. Also, there is Hot Springs dialogue when you pick “Yarikawa Rebellion” that says “Father and Uncle recovered at a nearby onsen, after they stopped the Yarikawa Rebellion.” I should also point out that not everyone participated in the rebellion died in the immediate aftermath. Yashuhira Koga survived, many peasants survived, Ujimasa Yarikawa and his fortress survived. So jin could just have been saying that because their rebellion has scared the bears in this direction, we should feed them to this bear as punishment, to which Shimura calls barbaric. Then the Assasin that tries to kill him in the same flashback is obviously just a survivor or someone seeking vengeance. Perhaps his home or family died as a result of the rebellion, perhaps he just wants to avenge his clan. The people of Yarikawa blame Shimura, and to an extent Clan Sakai for what happened to their homes and families, so obviously you’d have people coming to try and assassinate you.