I'm really not trying to be a Disney apologist here -- because, in reality, I'm far from it. But I think you're being a little over-dramatic here.
There's really not much awkwardness. A Tron themed coaster in Tomorrowland will always be a rad idea and provide a great design aesthetic for the area no matter how well the sequel performed or even if it never had come out in the first place. Fanboys have been wanting a Tron attraction since the original came out in the 80s and were teased with the speed tunnel. And as for Pirates having connective tiefs to the movie, who cares? How is that any better/worse than having connective ties to a 50 year-old theme park ride made in the 60s featuring the vocal talent of Tony the Tiger and Boris Badenov?
Short of Jack Sparrow (which, by now, has overcome 'flavor of the day' character status), it's not like Disney is throwing in a bunch of characters who we closely associate with actors from a certain era. You don't see Jeff Bridges anywhere in Tron nor are audiences going to look at Davy Jones and say, "Oh hey, that's Bill Nighy... what's he doing here!?" It's not like they're sticking Orlando Bloom and Keira Knightley in scenes. The only difference is that the attraction now features some characters that already resonate with audiences and have actual depth/backstories to them.
And this is coming from someone who absolutely hates having Jack Sparrow in the originals. It's definitely awkward to shoehorn the character into a story where he didn't exist previously, but it's another to build him into an attraction from the beginning in a way that makes sense.