Networks do that with every show that changes show runner. Damage control, nothing less and nothing more. Walking Dead did the same when Darabont was fired and replaced with Mazzara.
You're right. I work in PR (not TV-related, of course), and that's pretty standard operating procedure for any company to let staff know how to respond to anything negative in the news. I'm a big Dan Harmon fan, but that memo's pretty benign. Hard to be bent out of shape about it.
This show is great. Disappointing to see them let go of Harmon just as I got into it though. Can't figure out how I hadn't heard of this thing until two weeks ago. Blazed through all three season now and I'm just stuck here twiddling my thumbs. :'(