From the original post text, the only part that 'surprises' me is the affirmation that "...All of the our councillors are newish with less than 2 years in their roles..."
The scenario as described (with the exception of the point highlighted above) is sadly familiar but more commonly associated with a deeply embedded resistance to change mentality.
A long standing clerk 'guiding' and 'shepherding' (alternately described as running the show entirely to their own satisfaction) coupled with commonly long standing (not in this example) Cllrs that have insufficient professional experience or local government competence to understand and implement proper procedures preferring instead to sit back and be 'told' what to do by the clerk.
Uh Oh - there goes the apple cart - along comes a 'new' Cllr who seeks to examine, question, heaven forbid, even challenge the status quo.... Never mind that they may have researched their questions, read the legislation and be expressing legitimate concerns, no, that won't do.
The default defence mechanism for those that may feel 'challenged' (whether that be the clerk wielding the common threat of Ind Trib, or other elements within the council feeling inadequate by their inaction) is to set out to isolate, ostracise and alienate the 'trouble maker.'
That certainly appears to be the nub of the question given the reference to "remove" the new Cllr.
Sadly, there never appears to be the will to adopt a more rational, considered, professional and sensible approach of actually embracing the questions of the impudent 'new comer' and examining if there is any merit in them. Indeed, there are no examples given within the OP of the type or style of question being presented by this up-start firebrand.
Adopting and instilling a more inclusive 'corporate improvement' approach where 'new' issues are taken on face value and always given proper objective bandwidth invariably heads off the inevitable entrenchment of attitudes and escalation of dissatisfaction which invariably lead to either the clerk or the Cllr escalating the problem.
The answer, as is so often the case, but too late in this example, is obvious. Embrace new ideas and suggestions to avoid the creation or escalation of a toxic environment where nobody wins.
The outcome in the example given (clerk resignation) is worse for all concerned than it might have been if there had been a more receptive and considered response to the concerns being raised by the 'new' Cllr. As a point of note, time served (as a Cllr) is of absolutely no relevance in determining competence or suitability. I'd be so bold as to suggest even (in certain cases), that the longer the time served as a Cllr the LESS suitable some incumbents actually become....
Joyous Easter all