There is legislation in place that entitles a clerk to join the LGPS, however the full council must pass a resolution to confirm their agreement at a full council meeting as councils are designating bodies. The national contracts which have been agreed by two sets of solicitors representing both councils and clerks specify the LGPS scheme, whilst the good employment guide also states the LGPS is the preference scheme for clerks of both parishes and towns.
Yes you could technically pass resolution of a different pension scheme, by resolving at a council meeting to join another lower paid scheme but whilst you may be complying with an obligation to provide a pension ,you may not be complying to equality and discrimination employment laws. A big problem if the clerk is unhappy about this. A Court case could cost the council in excess of the clerks salary. The hmrc website for small employers also states it is illegal to dissuade someone to give up their pension rights so I would tread carefully as it would be important that the clerk was happy with any arrangement.
A Council must precept all statutory employment costs in its annual budget and must ask for as much as meets its needs. If you consider that your district council and all its employees including £100,000 Directors automatically get enrolled on the LGPS then really her request is within reason, especially as some District Councillors also claim the LGPS.