The problem with anything non ADA compliant is it cannot be remodeled without either bringing it into compliance or having to provide something to give the experience to those who cannot access it. At Disneyland when they went to reopen the Sleeping Beauty walk through and the Submarines, since there was no way to making them fully accessible they had to create simulations where anyone who physically couldn't access the attraction could still see what was there through a presentation on screens.
Every time they remodel anything at Disney it is a HUGE problem to bring things up to current codes and ADA regulations which is why some things never get fixed. There is a certain percentage of remodel work that can be done to anything without having to make all the changes necessary.
Once again, I love TSI and the river boat and feel like they are some of the best features of Magic Kingdom, however looking logically I can see that the space they use might be better used. When every year Magic Kingdom grows attendance, the number of attractions offered and the physical space in the park has not grown to match. Personally, if I ran things at WDW I would grow by eliminating the parking lot between Main Street and Tomorrowland and use that for an expansion first, but TSI and Rivers of America are prime spots for growing the park.
Playing devil's advocate look at it his way, if they remove the river boat (or make it stationary as a restaurant or show or something), they could then connect TSI to the mainland with bridges (eliminating the rafts which are old and dirty and dangerous). This could mean TSI could be updated and made ADA compliant. This could also mean that the back half of the river could be filled in for a huge expansion, but (just as importantly) it could mean they could build a back pathway connecting the dead end in front of the Haunted Mansion with the dead end in front of Big Thunder. This would be a HUGE improvement in traffic flow (especially during parades) as well as just improving the chaotic traffic between Splash Mountain, BTMRR, and Frontierland Station. As it is now that area is a cluster F all the time.