I agree about being open about things going on that are deceptive. But I would propose that any dealings with users/accounts that seem to only be present for flamebaiting/trolling/etc should be done privately by the mods, including any consequences. In the thread of today causing this fallout there was a lengthy post by Stefan, in effect describing a lot of evidence for why he was calling out certain “users” as sock puppets, etc. I’m not sure that that long post actually helped the case and its perception. It might have been better to suspend the relevant user accounts, make a post in the thread that this had been done, summarize the reasons and engage with the users in private for any followup.
I can see arguing it publicly as Stefan did is a form of transparency, but it also shows (in my opinion) a bit too much of personal engagement going on. In short, I like my mods to be definitely fair and transparent, but also somewhat above the normal discussions 
Just my 2 cents