Business wise, the company is in a bit of spending freeze outside of the capital projects, due to shanghai deal. While this would be a capitalized project, it's money that doesn't need to be spent. You are putting in Star Wars IP, and you have existing Star Wars IP. The muppets IP is in a facility that could be relocated if deemed worthy of retention, likely for less money than a re-theme of star tours. Even if you don't re-theme or move muppets you can make Star Tours work.
It costs money to retheme that, along with developing the cinematics. It's not a cheap proposition. Of the two options, a re-theme of muppets is the likely choice in terms of cost. Make it muppet star wars, and then you are in the clear.
In order to re-do star tours, it needs to be down for a while. I don't see them doing that, until after Star Wars is done. There just isn't enough rides to sustain the park in it's current state.