When it originally opened, the second floor had access to the 3D theater lobby. The flow of the pavilion was for guests to do the ride, go upstairs to Imageworks, then cross over to the movie.
So emergency evacuation could have gone into the theater lobby, then out.
So, even if someone says wheelchair accessibility was the reason for closing the second floor, I don't believe it and dont believe Disney would give that as an official reason for closing it.
The only article I have ever seen about accessibility even being a question said (without any proof) that OSHA requires accessibility if something is closed for a certain amount of time (without any proof off time period or even stating a time period). If you check on OSHA's website, they refer to ADA guidelines, which have some 'outs'.
But, there were elevators and a way to evacuate originally.
After they cut a large portion of the ride out, there was space for a smaller Imageworks. So, they had no reason to keep the original Imageworks open.
It also did not fit the re-themed attraction, which was a visit to the Imagination Institute.
Without renovating the 2nd floor, the remaining pieces (Imagination Institute and Honey I Shrunk the Audience went together. And, they did not have a big budget to work with.