Muppet Vision is safe from Galaxy's Edge expansion if for no other reason than that they would have to rip out and reroute the expensive rockwork queue of Rise of the Resistance in order to access the Muppet plot from within GE. I won't say for certain that Muppets is safe from harm, but it won't be death by lightsaber. Unless they move the Gateway to Galaxy's Edge closer to Baseline Tap House, which would also be expensive AND force them to close the main entry to the land while the work was done.
My guess is that we'd sooner see them turn the Muppets plot into something else, not Star Wars-related . . . but they did also just offer Muppets a little refurb to fix things up a little. Which doesn't automatically mean they wouldn't close it, but it inspires a little hope.
But still, add a Muppet Movie Ride to the park and they'd have my money day one.