Two things:
1) If they do close the attraction for any form of extended time, they better announce it far in advance. The main Harry Potter ride at IOA being closed could be a real "vacation ruiner" if they only announce it two weeks or a month in advance like they did with Hulk. I know I'd be hugely disappointed.
2) How about this really weird, blue-sky idea: if Forbidden Journey did close for a month or so to convert it to 3D, what if they kept the queue/Hogwarts tour open? Keep the entire line until the Sorting Hat room open (and cover up where the 3D glasses area is being placed, I guess), turn off the musion pre-shows, and just make it a walk-through attraction to see the inside of Hogwarts. The different paths in the queue could be changed to make one going through, one leaving. If they specify that "Harry Potter and the Forbidden Journey is currently closed for your future enjoyment, but the Hogwarts Castle Walking Tour is still open.", it could certainly put some of the guest complaints about the main ride being closed at ease.