Everything I've read shows that this is a real thing. That is was not a cover story for the colon surgery. The only way that he'll come back, is if there is an outpour of fan backlash, and the McMahons give in. But they've been looking to put a more youthful face on the announce team for a long time now.
It's unfortunate that J.R. was struck with Bell's Palsy twice, but it is a contributing factor to the reasonings of his termination.
We may see him back someday, but I don't think it'll be anytime in the near future.
Check out this past week's 'Byte This'. Coach and The King were on it, and they revealed some interesting insights.