This isn't actually an answer proper, but there's a few points where I suspect the process of well, all this could have run better. Hindsight is 20/20 , and this is not really a reflection on SE's moderation and administration processes. I'm posting this as a root access regular, and someone intimately familiar with the channel and its culture, and having heard one side of the issue. To mangle a quote from b5, understanding is a three edged sword, your side, their side and the truth, and I'm hoping this gives another perspective of this.
There wasn't any indication that an automatically triggered script was an issue before action was taken here. In general, the rules seem to be bot can't do anything a regular user can't. I suspect that's the real issue here, since it felt like a sudden decision, rather than a wider sitewide policy. We'd have had a lot less of a mess if we weren't working out what the lines were after action was taken. I do understand that the dev team explicitly didn't want this behaviour, but there was no way that the upstream or RA bot devs would have known of this.
Neither the regulars in the room, nor newbies had mentioned any issue with the bot. If we had felt so, we could have probably had a word with @allquixotic. The robogreeting was actually tweaked in consultationtweaked in consultation with the users, and for most part, the bot hasn't been a annoyance.
The first we knew of this was the bot getting suspended - which is a tiny bit like getting a telegram delivered through the roof by a swat team.
A little less shock and awe, might have been nice. @allquixotic has been very nice about tweaking his version of the chatbot (as time permits!), and this could have been probably handled with a little less drama (of which there was a little).