If the Starks have been aiming to contain the Boltons for thousands of years, why not just… you know, kill them all? They’ve had thousands of years to do it and there’s never been a single Bolton that was more decent than Roose or Ramsay.

Because exterminating an entire House, men, women and children all, is normally seen as tyranny; hence why everyone started seeing Aerys II as mad after the Defiance of Duskendale. And while it may cow your bannermen (see the Rains of Castamere), fear only goes so far as a motivator. 

But this line “there’s never been a single Bolton that was more decent than Roose or Ramsay” is complete hogwash. Yes, many if not most Boltons have been vicious brutes. But Domeric was a perfectly normal human, and I’m willing to bet there have been others before.