Has the Indiana Jones retheme ever even been mentioned by insiders as a possibility? Because it's so hard to imagine that actually happening, particularly with such an awesome attraction like Dinosaur. It would have to be an extremely expensive ordeal, far more expensive than simply fixing up Dinosaur to its full potential again. It's not like Splash Mountain, where there are other reasons for retheming it, so I just can't see Disney spending that much money to convert the ride. And if they did convert it, they would almost certainly cut aspects of the theming/experience to make it very inferior to the original attraction.
Unless the new Indy movie has him go back in time to the Cretaceous Period...then I'd be concerned they're actually going to do this.