Not everyone will want to ride it three times a day. I know TSMM is wildly popular, but that's primarily because it is a kid-friendly ride in a park with few such offerings. Some people will be satisfied with just one ride through.
In any case, all they have to do is limit the FPs in accordance with ride capacity. Maybe two per day max for that ride, instead of one? Maybe one per day unless you reserve well in advance?
Speaking of ride capacity, why aren't they addressing that by building new rides at DHS? Why, reportedly, have the Star Wars plans for DHS been put on hold? Oh right, I forgot. Their priority was to spend $1.5 billion on a new reservation system instead