The scenes themselves (and therefore the story) can be changed with ease. The track could be replaced to accomodate a different train or trains, but the ride path through the ball would stay the same... which would set some limits on the trains' physics. Not to say that good story-telling can't be thrilling, but that's not what people think of when the hear "thrill ride."
SE could be hacked to provide Pirates or Haunted Mansion type eerie thrills, but not ToT or M:S variety physical thrills.
Obviously, if they wanted a "real" thrill ride in that spot badly enough, they could just tear down the existing ball and build something else (I'm pretty sure that RCID's powers have dwindled to the point that not even WDW could get away with building an SE type ball, today...).
I don't think they'll tear out SE... but I also don't think they'll do the scene updates that they can actually do, in a practical sense. I think it's more likely that they'll let the same train run through the same scenes until something wears out enough that it's cheaper to seal up the ball than fix the ride.