The role of a clerk is complex and inter-personal relationships are critical. On the one hand, the clerk is the servant of the councillors, employed to manage their affairs in a "don't speak until you're spoken to" way. Alongside this, the clerk is the chief legal and financial officer of the council, responsible for guiding the council through the legal minefield. The clerk should also be the buffer zone, the peacekeeper in any conflict and the friendly gatekeeper between parishioners and the council. Some walk this tightrope better than others.
Opinions vary, but in my own rule book, joining debate is overstepping the mark, belittling parishioners is a hanging offence as there are no wrong questions, if the council hasn't debated the possibility of having a neighbourhood plan the clerk cannot express an opinion and if they have discussed it, the clerk should refer to the minutes of the meeting at which the discussion took place and finally, as I'm sure you know, the clerk can't flatly refuse anything!
It sounds as though she may have resigned, but isn't going to go away...